ENST00000649962.1:n.271+32445C>T

Variant names:

• chr1-73873484-G-A
• rs11210359
• ENST00000649962.1:n.271+32445C>T

Variant summary

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

The ENST00000649962.1(ENSG00000285778):​n.271+32445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,080 control chromosomes in the GnomAD database, including 27,466 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 0.59 (27466 hom., cov: 29)
• Consequence: ENSG00000285778 ENST00000649962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 7 publications found

Genes affected

ENSG00000285778 (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 = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649962.1. 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
	ENSG00000285778	ENST00000649962.1		n.271+32445C>T		intron	N/A
	ENSG00000285778	ENST00000667324.1		n.148+41645C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.588 AC: 88826 AN: 150962 Hom.: 27455 Cov.: 29

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.571

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.588 AC: 88873 AN: 151080 Hom.: 27466 Cov.: 29 AF XY: 0.595 AC XY: 43897 AN XY: 73758

African (AFR) AF: 0.386 AC: 15902 AN: 41164

American (AMR) AF: 0.676 AC: 10259 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2336 AN: 3448

East Asian (EAS) AF: 0.927 AC: 4733 AN: 5106

South Asian (SAS) AF: 0.830 AC: 3969 AN: 4784

European-Finnish (FIN) AF: 0.681 AC: 7083 AN: 10394

Middle Eastern (MID) AF: 0.562 AC: 163 AN: 290

European-Non Finnish (NFE) AF: 0.628 AC: 42545 AN: 67726

Other (OTH) AF: 0.605 AC: 1269 AN: 2096

Alfa AF: 0.624 Hom.: 89392

Bravo AF: 0.578

Asia WGS AF: 0.850 AC: 2955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.52
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11210359; hg19: chr1-74339167; COSMIC: COSV59956871;