10-15353182-T-C

Variant names:

• chr10-15353182-T-C
• rs11599615
• NM_001010924.2:c.97+17774A>G

Variant summary

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

The NM_001010924.2(FAM171A1):​c.97+17774A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,934 control chromosomes in the GnomAD database, including 13,698 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 0.42 (13698 hom., cov: 32)
• Consequence: FAM171A1 NM_001010924.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 4 publications found

Genes affected

FAM171A1 (HGNC:23522): (family with sequence similarity 171 member A1) Involved in regulation of cell shape and stress fiber assembly. Located in plasma membrane. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010924.2. 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
	FAM171A1	NM_001010924.2	MANE Select	c.97+17774A>G		intron	N/A	NP_001010924.1	Q5VUB5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM171A1	ENST00000378116.9	TSL:1 MANE Select	c.97+17774A>G		intron	N/A	ENSP00000367356.4	Q5VUB5
	FAM171A1	ENST00000946313.1		c.97+17774A>G		intron	N/A	ENSP00000616372.1
	FAM171A1	ENST00000946312.1		c.97+17774A>G		intron	N/A	ENSP00000616371.1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63840 AN: 151816 Hom.: 13692 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.435

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.420 AC: 63876 AN: 151934 Hom.: 13698 Cov.: 32 AF XY: 0.415 AC XY: 30780 AN XY: 74258

African (AFR) AF: 0.345 AC: 14295 AN: 41416

American (AMR) AF: 0.396 AC: 6039 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1088 AN: 5166

South Asian (SAS) AF: 0.315 AC: 1516 AN: 4808

European-Finnish (FIN) AF: 0.431 AC: 4537 AN: 10532

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33267 AN: 67968

Other (OTH) AF: 0.434 AC: 915 AN: 2106

Alfa AF: 0.459 Hom.: 51070

Bravo AF: 0.417

Asia WGS AF: 0.278 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.0
DANN	Benign	0.64
PhyloP100		1.0
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: rs11599615; hg19: chr10-15395181;