rs7594255

Variant names:

• chr2-164108310-T-C
• rs7594255
• ENST00000429636.1:n.196+142410A>G

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.196+142410A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,156 control chromosomes in the GnomAD database, including 1,979 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 0.14 (1979 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617
• Publications: 2 publications found

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.246 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
ENSG00000237844	ENST00000429636.1	n.196+142410A>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21573 AN: 152038 Hom.: 1978 Cov.: 32

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.142 AC: 21586 AN: 152156 Hom.: 1979 Cov.: 32 AF XY: 0.145 AC XY: 10754 AN XY: 74396

African (AFR) AF: 0.0545 AC: 2266 AN: 41540

American (AMR) AF: 0.252 AC: 3852 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3468

East Asian (EAS) AF: 0.0686 AC: 355 AN: 5176

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4820

European-Finnish (FIN) AF: 0.149 AC: 1577 AN: 10592

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11353 AN: 67972

Other (OTH) AF: 0.149 AC: 315 AN: 2116

Alfa AF: 0.141 Hom.: 892

Bravo AF: 0.144

Asia WGS AF: 0.144 AC: 503 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	16
DANN	Benign	0.83
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs7594255; hg19: chr2-164964820;