rs72844412

Variant names:

• chr2-85496886-G-A
• rs72844412
• ENST00000793246.1:n.141+19850C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-85496886-G-A
• chr2-85496886-G-C

Variant summary

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

The ENST00000793246.1(ENSG00000303258):​n.141+19850C>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 152,096 control chromosomes in the GnomAD database, including 3,074 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 (3074 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793246.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303258	ENST00000793246.1		n.141+19850C>T		intron	N/A
	ENSG00000303258	ENST00000793247.1		n.346+3147C>T		intron	N/A
	ENSG00000303258	ENST00000793248.1		n.339+3147C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29304 AN: 151978 Hom.: 3070 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.193 AC: 29328 AN: 152096 Hom.: 3074 Cov.: 31 AF XY: 0.191 AC XY: 14211 AN XY: 74342

African (AFR) AF: 0.144 AC: 5968 AN: 41510

American (AMR) AF: 0.179 AC: 2732 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.0396 AC: 205 AN: 5172

South Asian (SAS) AF: 0.0863 AC: 416 AN: 4822

European-Finnish (FIN) AF: 0.291 AC: 3076 AN: 10570

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15547 AN: 67966

Other (OTH) AF: 0.202 AC: 427 AN: 2114

Alfa AF: 0.192 Hom.: 1283

Bravo AF: 0.184

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.56
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs72844412; hg19: chr2-85724009;