rs2070996

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000253736 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.235

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

Splicing

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

Publications

LitVar

Other links and lift over

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