rs10494096

Variant names:

• chr1-108727780-G-A
• rs10494096
• NM_001144937.3:c.1112-28G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-108727780-G-A
• chr1-108727780-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144937.3(FNDC7):​c.1112-28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 1,610,268 control chromosomes in the GnomAD database, including 172,673 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.40 (13176 hom., cov: 30)
  • Exomes 𝑓: 0.46 (159497 hom.)
• Consequence: FNDC7 NM_001144937.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 5 publications found

Genes affected

FNDC7 (HGNC:26668): (fibronectin type III domain containing 7) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144937.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC7	NM_001144937.3	MANE Select	c.1112-28G>A		intron	N/A	NP_001138409.1	Q5VTL7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FNDC7	ENST00000370017.9	TSL:5 MANE Select	c.1112-28G>A		intron	N/A	ENSP00000359034.3	Q5VTL7
	FNDC7	ENST00000445274.1	TSL:1	c.437-28G>A		intron	N/A	ENSP00000405986.1	H7C2H6
	FNDC7	ENST00000932418.1		c.1112-852G>A		intron	N/A	ENSP00000602477.1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61020 AN: 151724 Hom.: 13169 Cov.: 30

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.385

GnomAD2 exomes AF: 0.428 AC: 106271 AN: 248426 AF XY: 0.437

Gnomad AFR exome AF: 0.267

Gnomad AMR exome AF: 0.357

Gnomad ASJ exome AF: 0.444

Gnomad EAS exome AF: 0.188

Gnomad FIN exome AF: 0.504

Gnomad NFE exome AF: 0.486

Gnomad OTH exome AF: 0.441

GnomAD4 exome AF: 0.463 AC: 675394 AN: 1458428 Hom.: 159497 Cov.: 44 AF XY: 0.464 AC XY: 336676 AN XY: 725348

African (AFR) AF: 0.260 AC: 8699 AN: 33448

American (AMR) AF: 0.355 AC: 15835 AN: 44652

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 11505 AN: 25826

East Asian (EAS) AF: 0.192 AC: 7633 AN: 39690

South Asian (SAS) AF: 0.460 AC: 39430 AN: 85798

European-Finnish (FIN) AF: 0.505 AC: 26851 AN: 53176

Middle Eastern (MID) AF: 0.436 AC: 2456 AN: 5636

European-Non Finnish (NFE) AF: 0.483 AC: 536500 AN: 1109938

Other (OTH) AF: 0.439 AC: 26485 AN: 60264

GnomAD4 genome AF: 0.402 AC: 61041 AN: 151840 Hom.: 13176 Cov.: 30 AF XY: 0.402 AC XY: 29821 AN XY: 74188

African (AFR) AF: 0.276 AC: 11426 AN: 41408

American (AMR) AF: 0.329 AC: 5022 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3470

East Asian (EAS) AF: 0.192 AC: 986 AN: 5146

South Asian (SAS) AF: 0.457 AC: 2197 AN: 4808

European-Finnish (FIN) AF: 0.508 AC: 5356 AN: 10536

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33062 AN: 67918

Other (OTH) AF: 0.381 AC: 801 AN: 2100

Alfa AF: 0.455 Hom.: 63443

Bravo AF: 0.383

Asia WGS AF: 0.307 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.51
PhyloP100		-0.065
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10494096; hg19: chr1-109270402; COSMIC: COSV54750861;