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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.738 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

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.738

Alfa AF: 0.683 Hom.: 4137

Bravo AF: 0.753

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1204028; hg19: chr7-122617785;