chr6-102331460-G-A

Variant names:

• chr6-102331460-G-A
• rs954551

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 0.735 in 151,760 control chromosomes in the GnomAD database, including 42,106 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 (42106 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.735 AC: 111510 AN: 151640 Hom.: 42081 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.735 AC: 111580 AN: 151760 Hom.: 42106 Cov.: 33 AF XY: 0.725 AC XY: 53799 AN XY: 74180

African (AFR) AF: 0.864 AC: 35851 AN: 41518

American (AMR) AF: 0.589 AC: 8968 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2611 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5166

South Asian (SAS) AF: 0.666 AC: 3208 AN: 4820

European-Finnish (FIN) AF: 0.618 AC: 6501 AN: 10524

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50282 AN: 67730

Other (OTH) AF: 0.741 AC: 1561 AN: 2106

Alfa AF: 0.742 Hom.: 54843

Bravo AF: 0.737

Asia WGS AF: 0.538 AC: 1869 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.34
DANN	Benign	0.40
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs954551; hg19: chr6-102779335;