rs1935683

chr6-112308352-T-C

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 0.141 in 152,162 control chromosomes in the GnomAD database, including 1,861 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 0.14 (1861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 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: 0.141 AC: 21380 AN: 152044 Hom.: 1855 Cov.: 32

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.141 AC: 21406 AN: 152162 Hom.: 1861 Cov.: 32 AF XY: 0.140 AC XY: 10444 AN XY: 74390

Gnomad4 AFR AF: 0.0604

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.158

Alfa AF: 0.160 Hom.: 328

Bravo AF: 0.152

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	2.9
Dann	Benign	0.91

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1935683; hg19: chr6-112629554;