6-110957720-G-C

Variant names:

• chr6-110957720-G-C
• rs9487562

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;