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. The variant received -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
• Publications: 22 publications found

Genes affected

ENSG00000234275 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425125.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234275	ENST00000425125.1	TSL:4	n.250+4108T>G		intron	N/A
	ENSG00000234275	ENST00000648803.1		n.52-6343T>G		intron	N/A
	ENSG00000234275	ENST00000650957.2		n.58-6343T>G		intron	N/A

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

African (AFR) AF: 0.779 AC: 32297 AN: 41444

American (AMR) AF: 0.575 AC: 8787 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1785 AN: 3466

East Asian (EAS) AF: 0.658 AC: 3395 AN: 5160

South Asian (SAS) AF: 0.489 AC: 2355 AN: 4820

European-Finnish (FIN) AF: 0.533 AC: 5623 AN: 10540

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30624 AN: 67934

Other (OTH) AF: 0.552 AC: 1162 AN: 2106

Alfa AF: 0.477 Hom.: 57958

Bravo AF: 0.580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7591996;

hg19: chr2-6461421;