7-66597948-A-T

Variant names:

• chr7-66597948-A-T
• rs10258739

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 0.546 in 152,086 control chromosomes in the GnomAD database, including 23,426 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 0.55 (23426 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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: 0.546 AC: 82951 AN: 151968 Hom.: 23400 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.546 AC: 83019 AN: 152086 Hom.: 23426 Cov.: 33 AF XY: 0.542 AC XY: 40303 AN XY: 74344

African (AFR) AF: 0.679 AC: 28163 AN: 41488

American (AMR) AF: 0.532 AC: 8125 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1469 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1798 AN: 5174

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4822

European-Finnish (FIN) AF: 0.476 AC: 5018 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34997 AN: 67994

Other (OTH) AF: 0.521 AC: 1102 AN: 2114

Alfa AF: 0.527 Hom.: 2684

Bravo AF: 0.556

Asia WGS AF: 0.382 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.44
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10258739; hg19: chr7-66062935; COSMIC: COSV107155001;