6-41322112-T-G

Variant names:

• chr6-41322112-T-G
• rs7772334

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;