6-110957720-G-C

Position:

• chr6-110957720-G-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 0.14 in 142,376 control chromosomes in the GnomAD database, including 1,734 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 (1734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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: 0.140 AC: 19876 AN: 142256 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0889

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.140 AC: 19930 AN: 142376 Hom.: 1734 Cov.: 32 AF XY: 0.138 AC XY: 9566 AN XY: 69186

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0888

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0508

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0944

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0367 Hom.: 29

Bravo AF: 0.174

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9487562; hg19: chr6-111278923;