rs3091338

Variant names:

• chr5-132067045-C-T
• rs3091338
• ENST00000731280.1:n.77+564C>T

Variant summary

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

The ENST00000731280.1(ENSG00000295603):​n.77+564C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,046 control chromosomes in the GnomAD database, including 8,047 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 0.30 (8047 hom., cov: 32)
• Consequence: ENSG00000295603 ENST00000731280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 40 publications found

Genes affected

ENSG00000295603 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731280.1. 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
	ENSG00000295603	ENST00000731280.1		n.77+564C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45581 AN: 151928 Hom.: 8047 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.300 AC: 45581 AN: 152046 Hom.: 8047 Cov.: 32 AF XY: 0.286 AC XY: 21256 AN XY: 74336

African (AFR) AF: 0.170 AC: 7066 AN: 41478

American (AMR) AF: 0.301 AC: 4607 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5184

South Asian (SAS) AF: 0.110 AC: 532 AN: 4816

European-Finnish (FIN) AF: 0.265 AC: 2807 AN: 10578

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28163 AN: 67924

Other (OTH) AF: 0.335 AC: 708 AN: 2114

Alfa AF: 0.366 Hom.: 21333

Bravo AF: 0.301

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.64
PhyloP100		-0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3091338;

hg19: chr5-131402738;

COSMIC: COSV57308689;