rs72844410

Variant names:

• chr2-85495883-T-C
• rs72844410
• ENST00000793246.1:n.141+20853A>G

Variant summary

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

The ENST00000793246.1(ENSG00000303258):​n.141+20853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,158 control chromosomes in the GnomAD database, including 2,605 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 0.18 (2605 hom., cov: 32)
• Consequence: ENSG00000303258 ENST00000793246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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+20853A>G		intron	N/A
	ENSG00000303258	ENST00000793247.1		n.346+4150A>G		intron	N/A
	ENSG00000303258	ENST00000793248.1		n.339+4150A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26858 AN: 152040 Hom.: 2604 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.177 AC: 26869 AN: 152158 Hom.: 2605 Cov.: 32 AF XY: 0.176 AC XY: 13067 AN XY: 74390

African (AFR) AF: 0.139 AC: 5771 AN: 41524

American (AMR) AF: 0.155 AC: 2374 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3472

East Asian (EAS) AF: 0.0391 AC: 203 AN: 5192

South Asian (SAS) AF: 0.0688 AC: 332 AN: 4824

European-Finnish (FIN) AF: 0.264 AC: 2794 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14140 AN: 67988

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.184 Hom.: 326

Bravo AF: 0.168

Asia WGS AF: 0.0650 AC: 227 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	9.8
DANN	Benign	0.45
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs72844410; hg19: chr2-85723006;