7-67367439-T-C

Position:

• chr7-67367439-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;