rs6708111

Positions:

• chr2-49797811-C-A

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 0.111 in 152,278 control chromosomes in the GnomAD database, including 1,092 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 0.11 (1092 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16964 AN: 152160 Hom.: 1091 Cov.: 33

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0654

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.111 AC: 16966 AN: 152278 Hom.: 1092 Cov.: 33 AF XY: 0.109 AC XY: 8142 AN XY: 74474

Gnomad4 AFR AF: 0.0750

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0646

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.123

Alfa AF: 0.127 Hom.: 298

Bravo AF: 0.108

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6708111; hg19: chr2-50024949;