rs1937596

Variant names:

• chr6-153703805-C-G
• rs1937596

Your query was ambiguous. Multiple possible variants found:

• chr6-153703805-C-G
• chr6-153703805-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.354 in 151,812 control chromosomes in the GnomAD database, including 10,097 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 0.35 (10097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 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: 0.354 AC: 53758 AN: 151694 Hom.: 10083 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.354 AC: 53803 AN: 151812 Hom.: 10097 Cov.: 32 AF XY: 0.351 AC XY: 26019 AN XY: 74164

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.373

Alfa AF: 0.161 Hom.: 277

Bravo AF: 0.373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937596; hg19: chr6-154024940;