rs1204028

Variant names:

• chr7-122977731-G-A
• rs1204028

Your query was ambiguous. Multiple possible variants found:

• chr7-122977731-G-A
• chr7-122977731-G-T

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 0.738 in 151,954 control chromosomes in the GnomAD database, including 42,334 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 0.74 (42334 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 1 publications found

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 = 0.891 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112005 AN: 151836 Hom.: 42268 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.738 AC: 112133 AN: 151954 Hom.: 42334 Cov.: 31 AF XY: 0.736 AC XY: 54618 AN XY: 74234

African (AFR) AF: 0.899 AC: 37287 AN: 41492

American (AMR) AF: 0.746 AC: 11382 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2366 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2739 AN: 5152

South Asian (SAS) AF: 0.672 AC: 3232 AN: 4808

European-Finnish (FIN) AF: 0.658 AC: 6933 AN: 10534

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45886 AN: 67932

Other (OTH) AF: 0.738 AC: 1552 AN: 2104

Alfa AF: 0.683 Hom.: 4137

Bravo AF: 0.753

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.25
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1204028; hg19: chr7-122617785;