6-121036637-T-G

Variant names:

• chr6-121036637-T-G
• rs1935946

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 0.558 in 152,104 control chromosomes in the GnomAD database, including 26,003 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 0.56 (26003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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: 0.558 AC: 84828 AN: 151988 Hom.: 25953 Cov.: 33

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.558 AC: 84936 AN: 152104 Hom.: 26003 Cov.: 33 AF XY: 0.563 AC XY: 41891 AN XY: 74368

African (AFR) AF: 0.765 AC: 31727 AN: 41500

American (AMR) AF: 0.626 AC: 9557 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1827 AN: 3472

East Asian (EAS) AF: 0.931 AC: 4817 AN: 5176

South Asian (SAS) AF: 0.688 AC: 3313 AN: 4816

European-Finnish (FIN) AF: 0.412 AC: 4354 AN: 10576

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

European-Non Finnish (NFE) AF: 0.408 AC: 27734 AN: 67976

Other (OTH) AF: 0.559 AC: 1180 AN: 2112

Alfa AF: 0.327 Hom.: 821

Bravo AF: 0.586

Asia WGS AF: 0.804 AC: 2795 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.041
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1935946; hg19: chr6-121357783;