rs10796285

Positions:

• chr10-15351310-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM171A1	NM_001010924.2	c.97+19646C>T		intron_variant		ENST00000378116.9
FAM171A1	XM_017015904.2	c.10+23198C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM171A1	ENST00000378116.9	c.97+19646C>T		intron_variant		1	NM_001010924.2	P1
FAM171A1	ENST00000455654.1	c.97+19646C>T		intron_variant		3

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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.429

Alfa AF: 0.422 Hom.: 17570

Bravo AF: 0.433

Asia WGS AF: 0.680 AC: 2359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.53
DANN	Benign	0.69

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: rs10796285; hg19: chr10-15393309;