rs4750628

Positions:

• chr10-15349183-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+21773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,000 control chromosomes in the GnomAD database, including 14,862 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 0.44 (14862 hom., cov: 32)
• Consequence: FAM171A1 NM_001010924.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM171A1	NM_001010924.2	c.97+21773C>T		intron_variant		ENST00000378116.9
FAM171A1	XM_017015904.2	c.10+25325C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM171A1	ENST00000378116.9	c.97+21773C>T		intron_variant		1	NM_001010924.2	P1
FAM171A1	ENST00000455654.1	c.97+21773C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66941 AN: 151882 Hom.: 14855 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.441 AC: 66983 AN: 152000 Hom.: 14862 Cov.: 32 AF XY: 0.434 AC XY: 32214 AN XY: 74284

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.446

Alfa AF: 0.472 Hom.: 22805

Bravo AF: 0.441

Asia WGS AF: 0.280 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.66

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: rs4750628; hg19: chr10-15391182;