7-67367439-T-C

Variant names:

• chr7-67367439-T-C
• rs956523

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 0.376 in 152,024 control chromosomes in the GnomAD database, including 11,520 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 0.38 (11520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57056 AN: 151908 Hom.: 11512 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.0871

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.376 AC: 57089 AN: 152024 Hom.: 11520 Cov.: 32 AF XY: 0.366 AC XY: 27207 AN XY: 74316

African (AFR) AF: 0.507 AC: 21014 AN: 41418

American (AMR) AF: 0.294 AC: 4490 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3470

East Asian (EAS) AF: 0.0873 AC: 453 AN: 5188

South Asian (SAS) AF: 0.311 AC: 1496 AN: 4818

European-Finnish (FIN) AF: 0.268 AC: 2832 AN: 10576

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24187 AN: 67968

Other (OTH) AF: 0.341 AC: 722 AN: 2116

Alfa AF: 0.354 Hom.: 12856

Bravo AF: 0.383

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.77
DANN	Benign	0.26
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs956523; hg19: chr7-66832426;