6-41287773-A-G

Variant names:

• chr6-41287773-A-G
• rs7768162

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 0.739 in 152,038 control chromosomes in the GnomAD database, including 42,333 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 0.74 (42333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.739 AC: 112325 AN: 151920 Hom.: 42283 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.739 AC: 112429 AN: 152038 Hom.: 42333 Cov.: 32 AF XY: 0.734 AC XY: 54584 AN XY: 74316

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.748

Alfa AF: 0.710 Hom.: 9767

Bravo AF: 0.759

Asia WGS AF: 0.557 AC: 1928 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7768162; hg19: chr6-41255511;