rs917235

Variant names:

• chr2-75598693-G-A
• rs917235
• ENST00000426657.1:n.*134G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-75598693-G-A
• chr2-75598693-G-T

Variant summary

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

The ENST00000426657.1(ENSG00000230477):​n.*134G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,098 control chromosomes in the GnomAD database, including 23,420 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 0.55 (23407 hom., cov: 32)
  • Exomes 𝑓: 0.52 (13 hom.)
• Consequence: ENSG00000230477 ENST00000426657.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• Publications: 15 publications found

Genes affected

ENSG00000230477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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
ENSG00000230477	ENST00000426657.1	n.*134G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84006 AN: 151890 Hom.: 23378 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.555

GnomAD4 exome AF: 0.522 AC: 47 AN: 90 Hom.: 13 AF XY: 0.533 AC XY: 32 AN XY: 60

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.700 AC: 7 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.548 AC: 34 AN: 62

Other (OTH) AF: 0.214 AC: 3 AN: 14

GnomAD4 genome AF: 0.553 AC: 84098 AN: 152008 Hom.: 23407 Cov.: 32 AF XY: 0.556 AC XY: 41330 AN XY: 74314

African (AFR) AF: 0.595 AC: 24648 AN: 41454

American (AMR) AF: 0.575 AC: 8788 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1337 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5160

South Asian (SAS) AF: 0.590 AC: 2840 AN: 4812

European-Finnish (FIN) AF: 0.572 AC: 6045 AN: 10564

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35660 AN: 67948

Other (OTH) AF: 0.555 AC: 1172 AN: 2110

Alfa AF: 0.534 Hom.: 69484

Bravo AF: 0.552

Asia WGS AF: 0.644 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	9.3
DANN	Benign	0.75
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs917235; hg19: chr2-75825819;