10-15353182-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM171A1	NM_001010924.2	c.97+17774A>G		intron_variant		ENST00000378116.9
FAM171A1	XM_017015904.2	c.10+21326A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM171A1	ENST00000378116.9	c.97+17774A>G		intron_variant		1	NM_001010924.2	P1
FAM171A1	ENST00000455654.1	c.97+17774A>G		intron_variant		3

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

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.434

Alfa AF: 0.467 Hom.: 34100

Bravo AF: 0.417

Asia WGS AF: 0.278 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.0
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs11599615; hg19: chr10-15395181;