rs1847202

Variant names:

• chr3-72885220-T-C
• rs1847202
• ENST00000832110.1:n.244-1809T>C

Variant summary

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

The ENST00000832110.1(ENSG00000308164):​n.244-1809T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,076 control chromosomes in the GnomAD database, including 13,792 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 0.40 (13792 hom., cov: 32)
• Consequence: ENSG00000308164 ENST00000832110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 7 publications found

Genes affected

ENSG00000308164 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 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
ENSG00000308164	ENST00000832110.1	n.244-1809T>C		intron_variant	Intron 1 of 1
ENSG00000308164	ENST00000832111.1	n.312-1809T>C		intron_variant	Intron 2 of 2
ENSG00000308164	ENST00000832112.1	n.277-1809T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61333 AN: 151958 Hom.: 13756 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.404 AC: 61436 AN: 152076 Hom.: 13792 Cov.: 32 AF XY: 0.397 AC XY: 29534 AN XY: 74342

African (AFR) AF: 0.577 AC: 23936 AN: 41456

American (AMR) AF: 0.331 AC: 5050 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3466

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5186

South Asian (SAS) AF: 0.175 AC: 845 AN: 4830

European-Finnish (FIN) AF: 0.397 AC: 4202 AN: 10576

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25309 AN: 67988

Other (OTH) AF: 0.374 AC: 790 AN: 2110

Alfa AF: 0.406 Hom.: 3760

Bravo AF: 0.407

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1847202; hg19: chr3-72934371;