rs922075

Positions:

• chr3-48447994-A-G
• chr3-48447994-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130384.3(ATRIP):​c.247+902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,942 control chromosomes in the GnomAD database, including 19,715 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 0.49 (19715 hom., cov: 31)
• Consequence: ATRIP NM_130384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.62

Genes affected

ATRIP (HGNC:33499): (ATR interacting protein) This gene encodes an essential component of the DNA damage checkpoint. The encoded protein binds to single-stranded DNA coated with replication protein A. The protein also interacts with the ataxia telangiectasia and Rad3 related protein kinase, resulting in its accumulation at intranuclear foci induced by DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]

ATRIP-TREX1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATRIP	NM_130384.3	c.247+902A>G		intron_variant		ENST00000320211.10
ATRIP-TREX1	NR_153405.1	n.314+902A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATRIP	ENST00000320211.10	c.247+902A>G		intron_variant		1	NM_130384.3	P1

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74793 AN: 151824 Hom.: 19701 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.493 AC: 74840 AN: 151942 Hom.: 19715 Cov.: 31 AF XY: 0.502 AC XY: 37252 AN XY: 74278

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.518

Alfa AF: 0.402 Hom.: 1571

Bravo AF: 0.483

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
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: rs922075; hg19: chr3-48489398;