chr7-46202985-T-G

Variant names:

• chr7-46202985-T-G
• rs6964415

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 0.0945 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0946 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

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0293

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.0873

Gnomad4 OTH AF: 0.0859

Alfa AF: 0.0852 Hom.: 938

Bravo AF: 0.0926

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6964415; hg19: chr7-46242583;