chr3-187393195-G-A

Variant names:

• chr3-187393195-G-A
• rs2102860
• ENST00000785797.1:n.284-3590G>A

Variant summary

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

The ENST00000785797.1(ENSG00000302323):​n.284-3590G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 152,332 control chromosomes in the GnomAD database, including 67,820 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 0.94 (67820 hom., cov: 34)
• Consequence: ENSG00000302323 ENST00000785797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 5 publications found

Genes affected

ENSG00000302323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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
ENSG00000302323	ENST00000785797.1	n.284-3590G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143536 AN: 152214 Hom.: 67773 Cov.: 34

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.943 AC: 143641 AN: 152332 Hom.: 67820 Cov.: 34 AF XY: 0.943 AC XY: 70266 AN XY: 74482

African (AFR) AF: 0.900 AC: 37389 AN: 41558

American (AMR) AF: 0.967 AC: 14799 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3364 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5177 AN: 5192

South Asian (SAS) AF: 0.980 AC: 4730 AN: 4828

European-Finnish (FIN) AF: 0.953 AC: 10123 AN: 10622

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.954 AC: 64931 AN: 68032

Other (OTH) AF: 0.949 AC: 2009 AN: 2116

Alfa AF: 0.942 Hom.: 9939

Bravo AF: 0.941

Asia WGS AF: 0.979 AC: 3406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.64
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2102860; hg19: chr3-187110983;