6-100504998-C-T

Variant names:

• chr6-100504998-C-T
• rs240763

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 0.558 in 151,908 control chromosomes in the GnomAD database, including 25,575 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 0.56 (25575 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84639 AN: 151790 Hom.: 25541 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.558 AC: 84723 AN: 151908 Hom.: 25575 Cov.: 31 AF XY: 0.553 AC XY: 41033 AN XY: 74230

African (AFR) AF: 0.815 AC: 33756 AN: 41442

American (AMR) AF: 0.418 AC: 6383 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1551 AN: 3462

East Asian (EAS) AF: 0.550 AC: 2831 AN: 5150

South Asian (SAS) AF: 0.494 AC: 2371 AN: 4804

European-Finnish (FIN) AF: 0.450 AC: 4744 AN: 10536

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31492 AN: 67938

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.561 Hom.: 14675

Bravo AF: 0.565

Asia WGS AF: 0.514 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.65
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs240763; hg19: chr6-100952874;