rs10796285

Variant names:

• chr10-15351310-G-A
• rs10796285
• NM_001010924.2:c.97+19646C>T

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+19646C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,938 control chromosomes in the GnomAD database, including 14,792 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 0.43 (14792 hom., cov: 32)
• Consequence: FAM171A1 NM_001010924.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM171A1	NM_001010924.2	MANE Select	c.97+19646C>T		intron	N/A	NP_001010924.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM171A1	ENST00000378116.9	TSL:1 MANE Select	c.97+19646C>T		intron	N/A	ENSP00000367356.4
	FAM171A1	ENST00000455654.1	TSL:3	c.97+19646C>T		intron	N/A	ENSP00000407796.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65843 AN: 151820 Hom.: 14773 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.434 AC: 65903 AN: 151938 Hom.: 14792 Cov.: 32 AF XY: 0.442 AC XY: 32829 AN XY: 74236

African (AFR) AF: 0.374 AC: 15495 AN: 41438

American (AMR) AF: 0.505 AC: 7703 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1410 AN: 3468

East Asian (EAS) AF: 0.785 AC: 4044 AN: 5152

South Asian (SAS) AF: 0.634 AC: 3055 AN: 4816

European-Finnish (FIN) AF: 0.436 AC: 4594 AN: 10542

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28233 AN: 67958

Other (OTH) AF: 0.429 AC: 905 AN: 2112

Alfa AF: 0.422 Hom.: 22426

Bravo AF: 0.433

Asia WGS AF: 0.680 AC: 2359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.53
DANN	Benign	0.69
PhyloP100		-0.12
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: rs10796285; hg19: chr10-15393309;