chr3-187204160-A-G

Variant names:

• chr3-187204160-A-G
• rs9872701
• ENST00000356133.3:n.345-314T>C

Variant summary

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

The ENST00000356133.3(ENSG00000198491):​n.345-314T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,968 control chromosomes in the GnomAD database, including 12,739 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 0.38 (12739 hom., cov: 31)
• Consequence: ENSG00000198491 ENST00000356133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 2 publications found

Genes affected

ENSG00000198491 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929106	NR_110052.1	n.345-314T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000198491	ENST00000356133.3	n.345-314T>C		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57061 AN: 151850 Hom.: 12744 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.375 AC: 57059 AN: 151968 Hom.: 12739 Cov.: 31 AF XY: 0.381 AC XY: 28318 AN XY: 74244

African (AFR) AF: 0.117 AC: 4844 AN: 41494

American (AMR) AF: 0.454 AC: 6934 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2926 AN: 5168

South Asian (SAS) AF: 0.471 AC: 2261 AN: 4802

European-Finnish (FIN) AF: 0.486 AC: 5111 AN: 10508

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32221 AN: 67944

Other (OTH) AF: 0.385 AC: 814 AN: 2114

Alfa AF: 0.446 Hom.: 10855

Bravo AF: 0.361

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.81
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs9872701; hg19: chr3-186921948;