rs7591996

Variant names:

• chr2-6321289-A-C
• rs7591996
• ENST00000425125.1:n.250+4108T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-6321289-A-C
• chr2-6321289-A-G
• chr2-6321289-A-T

Variant summary

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

The ENST00000425125.1(ENSG00000234275):​n.250+4108T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,950 control chromosomes in the GnomAD database, including 26,262 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 0.57 (26262 hom., cov: 32)
• Consequence: ENSG00000234275 ENST00000425125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

Genes affected

ENSG00000234275 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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
ENSG00000234275	ENST00000425125.1	n.250+4108T>G		intron_variant	Intron 1 of 2	4
ENSG00000234275	ENST00000648803.1	n.52-6343T>G		intron_variant	Intron 1 of 7
ENSG00000234275	ENST00000650957.2	n.58-6343T>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86383 AN: 151832 Hom.: 26200 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.569 AC: 86505 AN: 151950 Hom.: 26262 Cov.: 32 AF XY: 0.573 AC XY: 42542 AN XY: 74286

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.552

Alfa AF: 0.465 Hom.: 23416

Bravo AF: 0.580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7591996; hg19: chr2-6461421;