chr7-42457648-A-G

Variant names:

• chr7-42457648-A-G
• rs6977301

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 0.842 in 152,176 control chromosomes in the GnomAD database, including 54,533 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 0.84 (54533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 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: 0.842 AC: 128055 AN: 152058 Hom.: 54515 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.842 AC: 128119 AN: 152176 Hom.: 54533 Cov.: 32 AF XY: 0.837 AC XY: 62292 AN XY: 74404

African (AFR) AF: 0.745 AC: 30924 AN: 41486

American (AMR) AF: 0.841 AC: 12858 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2922 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3005 AN: 5168

South Asian (SAS) AF: 0.792 AC: 3818 AN: 4818

European-Finnish (FIN) AF: 0.889 AC: 9426 AN: 10604

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.916 AC: 62288 AN: 68024

Other (OTH) AF: 0.832 AC: 1755 AN: 2110

Alfa AF: 0.886 Hom.: 73765

Bravo AF: 0.830

Asia WGS AF: 0.658 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.43
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6977301; hg19: chr7-42497247;