rs7549830

Variant names:

• chr1-161718641-T-C
• rs7549830

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 0.185 in 152,206 control chromosomes in the GnomAD database, including 3,289 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 0.18 (3289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 6 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 = 0.435 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: 0.184 AC: 28045 AN: 152088 Hom.: 3281 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.185 AC: 28085 AN: 152206 Hom.: 3289 Cov.: 33 AF XY: 0.184 AC XY: 13703 AN XY: 74404

African (AFR) AF: 0.297 AC: 12330 AN: 41512

American (AMR) AF: 0.101 AC: 1544 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2332 AN: 5176

South Asian (SAS) AF: 0.182 AC: 876 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1563 AN: 10600

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8789 AN: 68004

Other (OTH) AF: 0.149 AC: 316 AN: 2116

Alfa AF: 0.142 Hom.: 910

Bravo AF: 0.185

Asia WGS AF: 0.286 AC: 995 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	1.2
DANN	Benign	0.35
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7549830; hg19: chr1-161688431;