rs61117627

Variant names:

• chr6-137922563-G-A
• rs61117627

Your query was ambiguous. Multiple possible variants found:

• chr6-137922563-G-A
• chr6-137922563-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0264 in 152,118 control chromosomes in the GnomAD database, including 54 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 0.026 (54 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0264 (4014/152118) while in subpopulation SAS AF = 0.0332 (160/4822). AF 95% confidence interval is 0.029. There are 54 homozygotes in GnomAd4. There are 1895 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 54 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4011 AN: 152000 Hom.: 54 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0264 AC: 4014 AN: 152118 Hom.: 54 Cov.: 32 AF XY: 0.0255 AC XY: 1895 AN XY: 74392

African (AFR) AF: 0.0242 AC: 1003 AN: 41496

American (AMR) AF: 0.0229 AC: 350 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.0274 AC: 142 AN: 5182

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4822

European-Finnish (FIN) AF: 0.0167 AC: 177 AN: 10590

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0292 AC: 1988 AN: 67978

Other (OTH) AF: 0.0218 AC: 46 AN: 2114

Alfa AF: 0.0289 Hom.: 15

Bravo AF: 0.0256

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.57
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs61117627; hg19: chr6-138243700;