6-137104844-A-G

Variant names:

• chr6-137104844-A-G
• rs44450

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 0.547 in 151,940 control chromosomes in the GnomAD database, including 24,417 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 0.55 (24417 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

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: 0.547 AC: 83037 AN: 151822 Hom.: 24409 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.547 AC: 83068 AN: 151940 Hom.: 24417 Cov.: 31 AF XY: 0.553 AC XY: 41028 AN XY: 74244

African (AFR) AF: 0.315 AC: 13052 AN: 41432

American (AMR) AF: 0.651 AC: 9945 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3460 AN: 5146

South Asian (SAS) AF: 0.449 AC: 2158 AN: 4808

European-Finnish (FIN) AF: 0.741 AC: 7822 AN: 10556

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42974 AN: 67932

Other (OTH) AF: 0.561 AC: 1187 AN: 2114

Alfa AF: 0.589 Hom.: 9026

Bravo AF: 0.540

Asia WGS AF: 0.543 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.8
DANN	Benign	0.79
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs44450; hg19: chr6-137425981; COSMIC: COSV60283807;