7-69005492-T-C

Variant names:

• chr7-69005492-T-C
• rs6973814

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.822 AC: 34144 AN: 41516

American (AMR) AF: 0.942 AC: 14403 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5080 AN: 5168

South Asian (SAS) AF: 0.942 AC: 4539 AN: 4818

European-Finnish (FIN) AF: 0.920 AC: 9765 AN: 10610

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64325 AN: 68040

Other (OTH) AF: 0.932 AC: 1969 AN: 2112

Alfa AF: 0.895 Hom.: 24563

Bravo AF: 0.908

Asia WGS AF: 0.962 AC: 3346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.48
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs6973814; hg19: chr7-68470479;