chr9-97674313-G-A

Position:

• chr9-97674313-G-A

Variant summary

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

The XM_006717278.2(XPA):​c.772+1176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 144,646 control chromosomes in the GnomAD database, including 2,700 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 0.19 (2700 hom., cov: 32)
• Consequence: XPA XM_006717278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

XPA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XPA	XM_006717278.2	c.772+1176C>T		intron_variant			XP_006717341.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 27880 AN: 144554 Hom.: 2694 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.193 AC: 27919 AN: 144646 Hom.: 2700 Cov.: 32 AF XY: 0.193 AC XY: 13622 AN XY: 70686

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.0426

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.170

Alfa AF: 0.176 Hom.: 318

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2808676; hg19: chr9-100436595;