rs2070996

Variant names:

• chr5-172771497-G-A
• rs2070996
• ENST00000523005.1:n.70-5995G>A

Variant summary

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

The ENST00000523005.1(ENSG00000253736):​n.70-5995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,048 control chromosomes in the GnomAD database, including 3,729 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 0.21 (3729 hom., cov: 32)
• Consequence: ENSG00000253736 ENST00000523005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658
• Publications: 4 publications found

Genes affected

ENSG00000253736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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
ENSG00000253736	ENST00000523005.1	n.70-5995G>A		intron_variant	Intron 1 of 1	3
ENSG00000253736	ENST00000792668.1	n.-130G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31408 AN: 151932 Hom.: 3720 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.207 AC: 31428 AN: 152048 Hom.: 3729 Cov.: 32 AF XY: 0.210 AC XY: 15639 AN XY: 74338

African (AFR) AF: 0.112 AC: 4657 AN: 41506

American (AMR) AF: 0.266 AC: 4071 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2012 AN: 5136

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4824

European-Finnish (FIN) AF: 0.252 AC: 2663 AN: 10574

Middle Eastern (MID) AF: 0.255 AC: 74 AN: 290

European-Non Finnish (NFE) AF: 0.214 AC: 14532 AN: 67940

Other (OTH) AF: 0.235 AC: 497 AN: 2114

Alfa AF: 0.213 Hom.: 462

Bravo AF: 0.204

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.8
DANN	Benign	0.96
PhyloP100		0.66
PromoterAI		0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2070996; hg19: chr5-172198500; COSMIC: COSV53321260;