rs17257972

Variant names:

• chr1-118563989-G-A
• rs17257972
• ENST00000746228.1:n.270+243C>T

Variant summary

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

The ENST00000746228.1(ENSG00000297215):​n.270+243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,988 control chromosomes in the GnomAD database, including 11,637 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 0.35 (11637 hom., cov: 31)
• Consequence: ENSG00000297215 ENST00000746228.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 2 publications found

Genes affected

ENSG00000297215 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 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
ENSG00000297215	ENST00000746228.1	n.270+243C>T		intron_variant	Intron 1 of 4
ENSG00000297215	ENST00000746229.1	n.179-887C>T		intron_variant	Intron 2 of 3
ENSG00000297215	ENST00000746230.1	n.178-887C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53960 AN: 151870 Hom.: 11638 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.355 AC: 53946 AN: 151988 Hom.: 11637 Cov.: 31 AF XY: 0.352 AC XY: 26143 AN XY: 74280

African (AFR) AF: 0.124 AC: 5158 AN: 41498

American (AMR) AF: 0.349 AC: 5328 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3468

East Asian (EAS) AF: 0.154 AC: 794 AN: 5162

South Asian (SAS) AF: 0.382 AC: 1836 AN: 4810

European-Finnish (FIN) AF: 0.414 AC: 4369 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32939 AN: 67916

Other (OTH) AF: 0.403 AC: 849 AN: 2106

Alfa AF: 0.451 Hom.: 27239

Bravo AF: 0.337

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.17
DANN	Benign	0.65
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs17257972; hg19: chr1-119106612;