chr5-93876252-T-C

Position:

• chr5-93876252-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000395965.8(FAM172A):​c.786+5218A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,206 control chromosomes in the GnomAD database, including 62,532 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 0.90 (62532 hom., cov: 32)
• Consequence: FAM172A ENST00000395965.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90

Genes affected

FAM172A (HGNC:25365): (ARB2 cotranscriptional regulator A) Predicted to contribute to siRNA binding activity. Predicted to be involved in heterochromatin assembly by small RNA; neural crest cell development; and regulation of alternative mRNA splicing, via spliceosome. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM172A	NM_032042.6	c.786+5218A>G		intron_variant		ENST00000395965.8	NP_114431.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM172A	ENST00000395965.8	c.786+5218A>G		intron_variant		1	NM_032042.6	ENSP00000379294	P1

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137363 AN: 152088 Hom.: 62505 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.903 AC: 137439 AN: 152206 Hom.: 62532 Cov.: 32 AF XY: 0.907 AC XY: 67509 AN XY: 74426

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.928

Alfa AF: 0.913 Hom.: 4926

Bravo AF: 0.893

Asia WGS AF: 0.975 AC: 3388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	22
DANN	Benign	0.86

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: rs10514378; hg19: chr5-93211958;