rs7549888

Variant names:

• chr1-22677526-G-T
• rs7549888

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 0.53 in 152,004 control chromosomes in the GnomAD database, including 22,010 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 0.53 (22010 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.609 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: 0.531 AC: 80620 AN: 151886 Hom.: 22000 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.530 AC: 80637 AN: 152004 Hom.: 22010 Cov.: 33 AF XY: 0.528 AC XY: 39259 AN XY: 74310

African (AFR) AF: 0.420 AC: 17419 AN: 41426

American (AMR) AF: 0.619 AC: 9468 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1792 AN: 3472

East Asian (EAS) AF: 0.324 AC: 1672 AN: 5154

South Asian (SAS) AF: 0.370 AC: 1783 AN: 4816

European-Finnish (FIN) AF: 0.580 AC: 6132 AN: 10578

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40554 AN: 67950

Other (OTH) AF: 0.546 AC: 1154 AN: 2112

Alfa AF: 0.563 Hom.: 41997

Bravo AF: 0.532

Asia WGS AF: 0.383 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7549888; hg19: chr1-23004019;