rs258972

Variant names:

• chr5-6000471-A-G
• rs258972

Your query was ambiguous. Multiple possible variants found:

• chr5-6000471-A-G
• chr5-6000471-A-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 0.965 in 152,106 control chromosomes in the GnomAD database, including 70,906 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 0.97 (70906 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146670 AN: 151988 Hom.: 70850 Cov.: 29

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.965 AC: 146786 AN: 152106 Hom.: 70906 Cov.: 29 AF XY: 0.964 AC XY: 71701 AN XY: 74358

African (AFR) AF: 0.931 AC: 38603 AN: 41478

American (AMR) AF: 0.978 AC: 14962 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3400 AN: 3470

East Asian (EAS) AF: 0.868 AC: 4460 AN: 5138

South Asian (SAS) AF: 0.990 AC: 4765 AN: 4814

European-Finnish (FIN) AF: 0.972 AC: 10283 AN: 10580

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67124 AN: 68016

Other (OTH) AF: 0.965 AC: 2036 AN: 2110

Alfa AF: 0.975 Hom.: 14510

Bravo AF: 0.962

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs258972; hg19: chr5-6000584;