rs11210359

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-73873484-G-A
• chr1-73873484-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285778 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000285778	ENST00000649962.1	n.271+32445C>T		intron_variant	Intron 2 of 3
ENSG00000285778	ENST00000667324.1	n.148+41645C>T		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.605

Alfa AF: 0.638 Hom.: 37576

Bravo AF: 0.578

Asia WGS AF: 0.850 AC: 2955 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	0.69
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

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