rs6548238

Variant names:

• chr2-634905-T-C
• rs6548238

Your query was ambiguous. Multiple possible variants found:

• chr2-634905-T-C
• chr2-634905-T-G

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 0.852 in 152,124 control chromosomes in the GnomAD database, including 55,361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.85 (55361 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -1.90
• Publications: 188 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 (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.852 AC: 129546 AN: 152006 Hom.: 55318 Cov.: 31

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.852 AC: 129646 AN: 152124 Hom.: 55361 Cov.: 31 AF XY: 0.855 AC XY: 63550 AN XY: 74350

African (AFR) AF: 0.887 AC: 36829 AN: 41510

American (AMR) AF: 0.870 AC: 13302 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4748 AN: 5168

South Asian (SAS) AF: 0.861 AC: 4130 AN: 4798

European-Finnish (FIN) AF: 0.849 AC: 8982 AN: 10580

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56333 AN: 68002

Other (OTH) AF: 0.845 AC: 1781 AN: 2108

Alfa AF: 0.836 Hom.: 175042

Bravo AF: 0.854

Asia WGS AF: 0.894 AC: 3110 AN: 3478

ClinVar

ClinVar submissions

Significance: risk factor

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Obesity (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6548238;

hg19: chr2-634905;