rs72844414

Variant names:

• chr2-85496980-C-A
• rs72844414
• ENST00000793246.1:n.141+19756G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-85496980-C-A
• chr2-85496980-C-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+19756G>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 152,018 control chromosomes in the GnomAD database, including 3,076 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 (3076 hom., cov: 31)
• Consequence: ENSG00000303258 ENST00000793246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• 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=-0.75).
• 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+19756G>T		intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793247.1	n.346+3053G>T		intron_variant	Intron 1 of 1
ENSG00000303258	ENST00000793248.1	n.339+3053G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29346 AN: 151900 Hom.: 3072 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.193

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: 29370 AN: 152018 Hom.: 3076 Cov.: 31 AF XY: 0.192 AC XY: 14242 AN XY: 74296

African (AFR) AF: 0.144 AC: 5971 AN: 41476

American (AMR) AF: 0.179 AC: 2726 AN: 15258

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

East Asian (EAS) AF: 0.0471 AC: 244 AN: 5176

South Asian (SAS) AF: 0.0856 AC: 413 AN: 4824

European-Finnish (FIN) AF: 0.293 AC: 3081 AN: 10532

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

European-Non Finnish (NFE) AF: 0.229 AC: 15552 AN: 67966

Other (OTH) AF: 0.202 AC: 426 AN: 2110

Alfa AF: 0.197 Hom.: 1362

Bravo AF: 0.184

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.6
DANN	Benign	0.44
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs72844414; hg19: chr2-85724103;