rs472615

Variant names:

• chr6-153949921-T-A
• rs472615

Your query was ambiguous. Multiple possible variants found:

• chr6-153949921-T-A
• chr6-153949921-T-G

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 0.799 in 152,178 control chromosomes in the GnomAD database, including 48,971 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 0.80 (48971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.88 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: 0.799 AC: 121546 AN: 152060 Hom.: 48945 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.799 AC: 121620 AN: 152178 Hom.: 48971 Cov.: 32 AF XY: 0.802 AC XY: 59647 AN XY: 74390

African (AFR) AF: 0.888 AC: 36870 AN: 41526

American (AMR) AF: 0.833 AC: 12728 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3920 AN: 5182

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4822

European-Finnish (FIN) AF: 0.823 AC: 8710 AN: 10584

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50657 AN: 67994

Other (OTH) AF: 0.779 AC: 1646 AN: 2114

Alfa AF: 0.765 Hom.: 5561

Bravo AF: 0.804

Asia WGS AF: 0.757 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.83
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs472615; hg19: chr6-154271056;