6-110977022-A-G

Variant names:

• chr6-110977022-A-G
• rs9400442

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 0.247 in 152,106 control chromosomes in the GnomAD database, including 5,387 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 0.25 (5387 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.248 AC: 37619 AN: 151988 Hom.: 5388 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.247 AC: 37640 AN: 152106 Hom.: 5387 Cov.: 33 AF XY: 0.254 AC XY: 18911 AN XY: 74370

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.227

Alfa AF: 0.220 Hom.: 697

Bravo AF: 0.234

Asia WGS AF: 0.477 AC: 1660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9400442; hg19: chr6-111298225;