6-41322112-T-G

Position:

• chr6-41322112-T-G

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 0.613 in 151,956 control chromosomes in the GnomAD database, including 29,039 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 0.61 (29039 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41322112T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93000 AN: 151838 Hom.: 29012 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.613 AC: 93081 AN: 151956 Hom.: 29039 Cov.: 32 AF XY: 0.613 AC XY: 45547 AN XY: 74258

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.615

Alfa AF: 0.564 Hom.: 10699

Bravo AF: 0.627

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7772334; hg19: chr6-41289850;