7-69005492-T-C

Variant names:

• chr7-69005492-T-C
• rs6973814

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;