3-187600993-G-T

Variant names:

• chr3-187600993-G-T
• rs1376969
• ENST00000832464.1:n.446+23924G>T

Variant summary

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

The ENST00000832464.1(ENSG00000308202):​n.446+23924G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,068 control chromosomes in the GnomAD database, including 9,955 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 0.34 (9955 hom., cov: 32)
• Consequence: ENSG00000308202 ENST00000832464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 5 publications found

Genes affected

ENSG00000308202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832464.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308202	ENST00000832464.1		n.446+23924G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52260 AN: 151950 Hom.: 9944 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.344 AC: 52291 AN: 152068 Hom.: 9955 Cov.: 32 AF XY: 0.348 AC XY: 25879 AN XY: 74322

African (AFR) AF: 0.179 AC: 7431 AN: 41510

American (AMR) AF: 0.412 AC: 6290 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3071 AN: 5156

South Asian (SAS) AF: 0.384 AC: 1854 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4741 AN: 10558

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26554 AN: 67964

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.369 Hom.: 1927

Bravo AF: 0.336

Asia WGS AF: 0.437 AC: 1522 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0040
DANN	Benign	0.31
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1376969; hg19: chr3-187318781;