chr7-67961336-T-C

Position:

• chr7-67961336-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 0.0641 in 152,252 control chromosomes in the GnomAD database, including 481 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 0.064 (481 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 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: 0.0639 AC: 9715 AN: 152134 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0430

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0641 AC: 9764 AN: 152252 Hom.: 481 Cov.: 33 AF XY: 0.0676 AC XY: 5032 AN XY: 74442

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0430

Gnomad4 NFE AF: 0.0222

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0350 Hom.: 330

Bravo AF: 0.0683

Asia WGS AF: 0.169 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6961611; hg19: chr7-67426323;