chr1-73617352-C-T

Variant names:

• chr1-73617352-C-T
• rs2341263
• ENST00000752875.1:n.191+22G>A

Variant summary

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

The ENST00000752875.1(ENSG00000298086):​n.191+22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,980 control chromosomes in the GnomAD database, including 5,912 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 0.28 (5912 hom., cov: 32)
• Consequence: ENSG00000298086 ENST00000752875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 2 publications found

Genes affected

ENSG00000298086 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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
ENSG00000298086	ENST00000752875.1	n.191+22G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41890 AN: 151862 Hom.: 5903 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.276 AC: 41931 AN: 151980 Hom.: 5912 Cov.: 32 AF XY: 0.281 AC XY: 20849 AN XY: 74300

African (AFR) AF: 0.302 AC: 12502 AN: 41406

American (AMR) AF: 0.284 AC: 4344 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 716 AN: 3464

East Asian (EAS) AF: 0.111 AC: 571 AN: 5158

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4822

European-Finnish (FIN) AF: 0.361 AC: 3813 AN: 10572

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18012 AN: 67970

Other (OTH) AF: 0.262 AC: 551 AN: 2104

Alfa AF: 0.265 Hom.: 15773

Bravo AF: 0.273

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2341263; hg19: chr1-74083035;