rs7526034

Variant names:

• chr1-63121302-G-T
• rs7526034

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 0.139 in 152,016 control chromosomes in the GnomAD database, including 2,350 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 0.14 (2350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21203 AN: 151898 Hom.: 2355 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.139 AC: 21179 AN: 152016 Hom.: 2350 Cov.: 32 AF XY: 0.152 AC XY: 11254 AN XY: 74268

African (AFR) AF: 0.0316 AC: 1312 AN: 41484

American (AMR) AF: 0.130 AC: 1986 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2712 AN: 5162

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4812

European-Finnish (FIN) AF: 0.325 AC: 3422 AN: 10526

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9809 AN: 67968

Other (OTH) AF: 0.114 AC: 240 AN: 2112

Alfa AF: 0.143 Hom.: 4256

Bravo AF: 0.119

Asia WGS AF: 0.322 AC: 1114 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.4
DANN	Benign	0.80
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7526034; hg19: chr1-63586973;