rs2250603

Variant names:

• chr7-136286559-G-A
• rs2250603
• ENST00000435996.1:n.243-42423G>A

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.243-42423G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,074 control chromosomes in the GnomAD database, including 1,898 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 (1898 hom., cov: 32)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 2 publications found

Genes affected

ENSG00000232053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375523	NR_187956.1	n.275-42423G>A		intron_variant	Intron 2 of 4
LOC105375523	NR_187957.1	n.615-42423G>A		intron_variant	Intron 4 of 5
LOC105375523	NR_187960.1	n.615-42423G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232053	ENST00000435996.1	n.243-42423G>A		intron_variant	Intron 2 of 3	3
ENSG00000232053	ENST00000445293.6	n.615-42423G>A		intron_variant	Intron 4 of 6	5
ENSG00000232053	ENST00000657456.1	n.509-42423G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21888 AN: 151956 Hom.: 1885 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.144 AC: 21913 AN: 152074 Hom.: 1898 Cov.: 32 AF XY: 0.145 AC XY: 10746 AN XY: 74358

African (AFR) AF: 0.207 AC: 8597 AN: 41472

American (AMR) AF: 0.198 AC: 3032 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3470

East Asian (EAS) AF: 0.129 AC: 672 AN: 5190

South Asian (SAS) AF: 0.247 AC: 1191 AN: 4822

European-Finnish (FIN) AF: 0.0840 AC: 887 AN: 10558

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6797 AN: 67966

Other (OTH) AF: 0.150 AC: 317 AN: 2110

Alfa AF: 0.135 Hom.: 310

Bravo AF: 0.154

Asia WGS AF: 0.205 AC: 711 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs2250603; hg19: chr7-135971307;