rs7538501

Variant names:

• chr1-196932623-C-T
• rs7538501
• XR_007066779.1:n.257+834G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007066779.1(LOC105371675):​n.257+834G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,522 control chromosomes in the GnomAD database, including 2,881 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 0.17 (2881 hom., cov: 32)
• Consequence: LOC105371675 XR_007066779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 7 publications found

Genes affected

LOC105371675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371675	XR_007066779.1	n.257+834G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25363 AN: 151404 Hom.: 2878 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.167 AC: 25376 AN: 151522 Hom.: 2881 Cov.: 32 AF XY: 0.165 AC XY: 12233 AN XY: 74074

African (AFR) AF: 0.285 AC: 11693 AN: 41032

American (AMR) AF: 0.127 AC: 1927 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3466

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5168

South Asian (SAS) AF: 0.145 AC: 697 AN: 4822

European-Finnish (FIN) AF: 0.0928 AC: 981 AN: 10572

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9147 AN: 67948

Other (OTH) AF: 0.178 AC: 375 AN: 2108

Alfa AF: 0.139 Hom.: 1192

Bravo AF: 0.174

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.19
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7538501; hg19: chr1-196901753;