ENST00000648975.1:n.2421-1993C>T

Variant names:

• chr5-40480085-G-A
• rs6871834
• ENST00000648975.1:n.2421-1993C>T

Variant summary

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

The ENST00000648975.1(ENSG00000285616):​n.2421-1993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,930 control chromosomes in the GnomAD database, including 26,584 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 0.58 (26584 hom., cov: 31)
• Consequence: ENSG00000285616 ENST00000648975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 11 publications found

Genes affected

ENSG00000285616 (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 (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648975.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285616	ENST00000648975.1		n.2421-1993C>T		intron	N/A
	ENSG00000285552	ENST00000649444.1		n.120-6291G>A		intron	N/A
	ENSG00000285552	ENST00000649894.1		n.119+16405G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88281 AN: 151812 Hom.: 26571 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.581 AC: 88329 AN: 151930 Hom.: 26584 Cov.: 31 AF XY: 0.575 AC XY: 42668 AN XY: 74250

African (AFR) AF: 0.485 AC: 20077 AN: 41438

American (AMR) AF: 0.576 AC: 8780 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2212 AN: 3464

East Asian (EAS) AF: 0.237 AC: 1224 AN: 5164

South Asian (SAS) AF: 0.481 AC: 2317 AN: 4818

European-Finnish (FIN) AF: 0.577 AC: 6086 AN: 10552

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45455 AN: 67940

Other (OTH) AF: 0.603 AC: 1267 AN: 2102

Alfa AF: 0.631 Hom.: 7716

Bravo AF: 0.578

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.53
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6871834; hg19: chr5-40480187;