7-64447032-C-T

Variant names:

• chr7-64447032-C-T
• rs1842055

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 0.634 in 152,032 control chromosomes in the GnomAD database, including 31,686 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 0.63 (31686 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 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: 0.634 AC: 96310 AN: 151914 Hom.: 31641 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.634 AC: 96410 AN: 152032 Hom.: 31686 Cov.: 33 AF XY: 0.633 AC XY: 47018 AN XY: 74306

African (AFR) AF: 0.819 AC: 33974 AN: 41506

American (AMR) AF: 0.555 AC: 8479 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1791 AN: 3462

East Asian (EAS) AF: 0.677 AC: 3498 AN: 5168

South Asian (SAS) AF: 0.526 AC: 2539 AN: 4824

European-Finnish (FIN) AF: 0.612 AC: 6444 AN: 10536

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37690 AN: 67942

Other (OTH) AF: 0.589 AC: 1241 AN: 2108

Alfa AF: 0.624 Hom.: 7217

Bravo AF: 0.639

Asia WGS AF: 0.662 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.13
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1842055; hg19: chr7-63907410;