7-69005492-T-C

Position:

• chr7-69005492-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 0.912 in 152,224 control chromosomes in the GnomAD database, including 63,529 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 0.91 (63529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 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: 0.912 AC: 138694 AN: 152106 Hom.: 63497 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.912 AC: 138780 AN: 152224 Hom.: 63529 Cov.: 32 AF XY: 0.912 AC XY: 67873 AN XY: 74418

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.932

Alfa AF: 0.922 Hom.: 10055

Bravo AF: 0.908

Asia WGS AF: 0.962 AC: 3346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6973814; hg19: chr7-68470479;