rs72844411

Variant names:

• chr2-85496736-G-A
• rs72844411
• ENST00000793246.1:n.141+20000C>T

Variant summary

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

The ENST00000793246.1(ENSG00000303258):​n.141+20000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,110 control chromosomes in the GnomAD database, including 3,077 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 0.19 (3077 hom., cov: 31)
• Consequence: ENSG00000303258 ENST00000793246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 2 publications found

Genes affected

ENSG00000303258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 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
ENSG00000303258	ENST00000793246.1	n.141+20000C>T		intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793247.1	n.346+3297C>T		intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793248.1	n.339+3297C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29312 AN: 151992 Hom.: 3073 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.193 AC: 29342 AN: 152110 Hom.: 3077 Cov.: 31 AF XY: 0.191 AC XY: 14228 AN XY: 74350

African (AFR) AF: 0.144 AC: 5993 AN: 41514

American (AMR) AF: 0.178 AC: 2717 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3468

East Asian (EAS) AF: 0.0393 AC: 204 AN: 5190

South Asian (SAS) AF: 0.0852 AC: 410 AN: 4810

European-Finnish (FIN) AF: 0.293 AC: 3093 AN: 10562

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15543 AN: 67986

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.205 Hom.: 398

Bravo AF: 0.183

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.33
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs72844411; hg19: chr2-85723859; COSMIC: COSV71724935;