7-67367439-T-C

Variant names:

• chr7-67367439-T-C
• rs956523

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 0.376 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.376 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

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.0873

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.341

Alfa AF: 0.347 Hom.: 9444

Bravo AF: 0.383

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs956523; hg19: chr7-66832426;