rs1937596

chr6-153703805-C-Gchr6-153703805-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;