rs1508212

Variant names:

• chr16-65245483-A-G
• rs1508212
• ENST00000562656.1:n.126-6241A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-65245483-A-G
• chr16-65245483-A-T

Variant summary

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

The ENST00000562656.1(ENSG00000260364):​n.126-6241A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,076 control chromosomes in the GnomAD database, including 31,570 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 0.64 (31570 hom., cov: 33)
• Consequence: ENSG00000260364 ENST00000562656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 2 publications found

Genes affected

ENSG00000260364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903780	XR_007065224.1	n.1138-6241A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260364	ENST00000562656.1	n.126-6241A>G		intron_variant	Intron 1 of 4	3
ENSG00000260364	ENST00000764865.1	n.194+12303A>G		intron_variant	Intron 1 of 2
ENSG00000260364	ENST00000764866.1	n.1177+12303A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97112 AN: 151958 Hom.: 31551 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.639 AC: 97180 AN: 152076 Hom.: 31570 Cov.: 33 AF XY: 0.629 AC XY: 46727 AN XY: 74336

African (AFR) AF: 0.713 AC: 29590 AN: 41494

American (AMR) AF: 0.584 AC: 8915 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2412 AN: 3466

East Asian (EAS) AF: 0.394 AC: 2036 AN: 5174

South Asian (SAS) AF: 0.542 AC: 2617 AN: 4826

European-Finnish (FIN) AF: 0.554 AC: 5851 AN: 10564

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43471 AN: 67972

Other (OTH) AF: 0.645 AC: 1359 AN: 2108

Alfa AF: 0.637 Hom.: 130105

Bravo AF: 0.644

Asia WGS AF: 0.503 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.59
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1508212; hg19: chr16-65279386;