rs6845297

Variant names:

• chr4-74393688-G-A
• rs6845297

Your query was ambiguous. Multiple possible variants found:

• chr4-74393688-G-A
• chr4-74393688-G-T

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 0.479 in 151,872 control chromosomes in the GnomAD database, including 19,941 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 0.48 (19941 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.479 AC: 72672 AN: 151756 Hom.: 19939 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.479 AC: 72682 AN: 151872 Hom.: 19941 Cov.: 31 AF XY: 0.480 AC XY: 35618 AN XY: 74224

African (AFR) AF: 0.211 AC: 8748 AN: 41414

American (AMR) AF: 0.566 AC: 8637 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1597 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1960 AN: 5138

South Asian (SAS) AF: 0.346 AC: 1659 AN: 4796

European-Finnish (FIN) AF: 0.661 AC: 6979 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41249 AN: 67928

Other (OTH) AF: 0.517 AC: 1090 AN: 2110

Alfa AF: 0.554 Hom.: 36594

Bravo AF: 0.465

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.51
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6845297; hg19: chr4-75259405;