6-86298465-T-G

Variant names:

• chr6-86298465-T-G
• rs1891754

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 0.661 in 151,974 control chromosomes in the GnomAD database, including 33,422 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 0.66 (33422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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: 0.661 AC: 100443 AN: 151856 Hom.: 33396 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.661 AC: 100526 AN: 151974 Hom.: 33422 Cov.: 32 AF XY: 0.663 AC XY: 49231 AN XY: 74284

African (AFR) AF: 0.663 AC: 27477 AN: 41442

American (AMR) AF: 0.633 AC: 9652 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2029 AN: 3468

East Asian (EAS) AF: 0.902 AC: 4660 AN: 5164

South Asian (SAS) AF: 0.692 AC: 3332 AN: 4816

European-Finnish (FIN) AF: 0.634 AC: 6697 AN: 10564

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44673 AN: 67962

Other (OTH) AF: 0.614 AC: 1295 AN: 2110

Alfa AF: 0.583 Hom.: 2002

Bravo AF: 0.664

Asia WGS AF: 0.742 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1891754;

hg19: chr6-87008183;

COSMIC: COSV53433946;