rs3764220

Variant names:

• chr15-51679861-A-G
• rs3764220
• ENST00000746672.1:n.346+1223T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-51679861-A-G
• chr15-51679861-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000746672.1(ENSG00000297267):​n.346+1223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 152,260 control chromosomes in the GnomAD database, including 568 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 0.052 (568 hom., cov: 32)
• Consequence: ENSG00000297267 ENST00000746672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 5 publications found

Genes affected

ENSG00000297267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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
ENSG00000297267	ENST00000746672.1	n.346+1223T>C		intron_variant	Intron 1 of 1
ENSG00000297287	ENST00000746809.1	n.149-1064A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7967 AN: 152142 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0954

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000412

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0524 AC: 7984 AN: 152260 Hom.: 568 Cov.: 32 AF XY: 0.0518 AC XY: 3854 AN XY: 74468

African (AFR) AF: 0.168 AC: 6972 AN: 41512

American (AMR) AF: 0.0229 AC: 350 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.0952 AC: 494 AN: 5188

South Asian (SAS) AF: 0.0122 AC: 59 AN: 4830

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10614

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000412 AC: 28 AN: 68026

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0156 Hom.: 184

Bravo AF: 0.0590

Asia WGS AF: 0.0520 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.80
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs3764220; hg19: chr15-51972058;