rs7517126

Variant names:

• chr1-196871142-A-G
• rs7517126

Variant summary

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

The variant allele was found at a frequency of 0.227 in 151,348 control chromosomes in the GnomAD database, including 6,458 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 0.23 (6458 hom., cov: 32)
• Consequence: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 11 publications found

Genes affected

LOC100996886 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996886		n.196871142A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.426+12738A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34389 AN: 151232 Hom.: 6448 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.227 AC: 34425 AN: 151348 Hom.: 6458 Cov.: 32 AF XY: 0.224 AC XY: 16554 AN XY: 73980

African (AFR) AF: 0.492 AC: 20141 AN: 40932

American (AMR) AF: 0.148 AC: 2254 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3472

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5162

South Asian (SAS) AF: 0.161 AC: 776 AN: 4812

European-Finnish (FIN) AF: 0.0946 AC: 995 AN: 10522

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9229 AN: 67928

Other (OTH) AF: 0.221 AC: 464 AN: 2104

Alfa AF: 0.164 Hom.: 1447

Bravo AF: 0.242

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.36
PhyloP100		-1.6
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: rs7517126; hg19: chr1-196840272;