chr7-46202985-T-G

Variant names:

• chr7-46202985-T-G
• rs6964415

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 0.0945 in 152,170 control chromosomes in the GnomAD database, including 763 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 0.094 (763 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14380 AN: 152052 Hom.: 765 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.0868

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

GnomAD4 genome AF: 0.0945 AC: 14375 AN: 152170 Hom.: 763 Cov.: 33 AF XY: 0.0961 AC XY: 7153 AN XY: 74400

African (AFR) AF: 0.100 AC: 4165 AN: 41528

American (AMR) AF: 0.0692 AC: 1058 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3468

East Asian (EAS) AF: 0.152 AC: 783 AN: 5164

South Asian (SAS) AF: 0.0293 AC: 141 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1634 AN: 10602

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5937 AN: 67994

Other (OTH) AF: 0.0859 AC: 181 AN: 2108

Alfa AF: 0.0870 Hom.: 2048

Bravo AF: 0.0926

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.75
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs6964415; hg19: chr7-46242583;