chr6-76198819-T-G

Variant names:

• chr6-76198819-T-G
• rs1486039

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.745 in 151,570 control chromosomes in the GnomAD database, including 42,609 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 (42609 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.745 AC: 112767 AN: 151452 Hom.: 42579 Cov.: 30

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.745 AC: 112849 AN: 151570 Hom.: 42609 Cov.: 30 AF XY: 0.741 AC XY: 54834 AN XY: 74032

African (AFR) AF: 0.634 AC: 26221 AN: 41356

American (AMR) AF: 0.720 AC: 10917 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2749 AN: 3464

East Asian (EAS) AF: 0.589 AC: 2991 AN: 5074

South Asian (SAS) AF: 0.759 AC: 3654 AN: 4816

European-Finnish (FIN) AF: 0.757 AC: 7976 AN: 10542

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55633 AN: 67842

Other (OTH) AF: 0.762 AC: 1610 AN: 2112

Alfa AF: 0.795 Hom.: 148714

Bravo AF: 0.736

Asia WGS AF: 0.663 AC: 2304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1486039; hg19: chr6-76908536;