rs11210359

chr1-73873484-G-Achr1-73873484-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, non coding transcript 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: ENST00000649962.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649962.1	n.271+32445C>T		intron_variant, non_coding_transcript_variant
	ENST00000667324.1	n.148+41645C>T		intron_variant, non_coding_transcript_variant

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;