ENST00000662001.2:n.203-18936C>T

Variant names:

• chr7-24338421-G-A
• rs2521634
• ENST00000662001.2:n.203-18936C>T

Variant summary

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

The ENST00000662001.2(ENSG00000228944):​n.203-18936C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,966 control chromosomes in the GnomAD database, including 4,953 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 0.25 (4953 hom., cov: 31)
• Consequence: ENSG00000228944 ENST00000662001.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 9 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662001.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228944	ENST00000662001.2		n.203-18936C>T		intron	N/A
	ENSG00000228944	ENST00000718234.1		n.191-18936C>T		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.213-18936C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37722 AN: 151848 Hom.: 4952 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.248 AC: 37758 AN: 151966 Hom.: 4953 Cov.: 31 AF XY: 0.243 AC XY: 18084 AN XY: 74276

African (AFR) AF: 0.325 AC: 13467 AN: 41398

American (AMR) AF: 0.188 AC: 2870 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3472

East Asian (EAS) AF: 0.182 AC: 940 AN: 5174

South Asian (SAS) AF: 0.172 AC: 829 AN: 4810

European-Finnish (FIN) AF: 0.199 AC: 2100 AN: 10572

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16219 AN: 67960

Other (OTH) AF: 0.243 AC: 513 AN: 2110

Alfa AF: 0.234 Hom.: 12408

Bravo AF: 0.252

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.66
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2521634; hg19: chr7-24378040;