chr7-44561096-G-A

Variant names:

• chr7-44561096-G-A
• rs217386

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 0.405 in 151,984 control chromosomes in the GnomAD database, including 13,153 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 0.40 (13153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61529 AN: 151866 Hom.: 13154 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.405 AC: 61553 AN: 151984 Hom.: 13153 Cov.: 32 AF XY: 0.392 AC XY: 29140 AN XY: 74292

African (AFR) AF: 0.471 AC: 19479 AN: 41396

American (AMR) AF: 0.339 AC: 5173 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1727 AN: 3472

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5176

South Asian (SAS) AF: 0.282 AC: 1365 AN: 4832

European-Finnish (FIN) AF: 0.300 AC: 3178 AN: 10576

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29017 AN: 67948

Other (OTH) AF: 0.434 AC: 916 AN: 2110

Alfa AF: 0.408 Hom.: 8377

Bravo AF: 0.412

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs217386; hg19: chr7-44600695;