rs960902

Variant names:

• chr2-37504522-G-A
• rs960902
• ENST00000668683.1:n.255-19447G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-37504522-G-A
• chr2-37504522-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668683.1(ENSG00000287316):​n.255-19447G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,814 control chromosomes in the GnomAD database, including 20,193 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 0.51 (20193 hom., cov: 31)
• Consequence: ENSG00000287316 ENST00000668683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

ENSG00000287316 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 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
ENSG00000287316	ENST00000668683.1	n.255-19447G>A		intron_variant	Intron 2 of 2
LINC03063	ENST00000686061.1	n.121+14941G>A		intron_variant	Intron 1 of 2
LINC03063	ENST00000689279.1	n.121+14941G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77953 AN: 151696 Hom.: 20172 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.514 AC: 78025 AN: 151814 Hom.: 20193 Cov.: 31 AF XY: 0.518 AC XY: 38413 AN XY: 74186

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.508

Alfa AF: 0.496 Hom.: 38050

Bravo AF: 0.518

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs960902; hg19: chr2-37731665;