rs11662010

Variant names:

• chr18-77249441-A-G
• rs11662010
• ENST00000844041.1:n.276T>C

Variant summary

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

The ENST00000844041.1(ENSG00000309801):​n.276T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,942 control chromosomes in the GnomAD database, including 13,483 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 0.42 (13483 hom., cov: 32)
• Consequence: ENSG00000309801 ENST00000844041.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 3 publications found

Genes affected

ENSG00000309801 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844041.1. 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
	ENSG00000309801	ENST00000844041.1		n.276T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000309801	ENST00000844042.1		n.229T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000309801	ENST00000844037.1		n.162+1407T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63281 AN: 151824 Hom.: 13472 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.417 AC: 63320 AN: 151942 Hom.: 13483 Cov.: 32 AF XY: 0.414 AC XY: 30718 AN XY: 74268

African (AFR) AF: 0.401 AC: 16626 AN: 41438

American (AMR) AF: 0.340 AC: 5191 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1450 AN: 5154

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4820

European-Finnish (FIN) AF: 0.400 AC: 4226 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31099 AN: 67928

Other (OTH) AF: 0.419 AC: 882 AN: 2106

Alfa AF: 0.441 Hom.: 3613

Bravo AF: 0.412

Asia WGS AF: 0.298 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-1.8
PromoterAI		-0.066	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11662010; hg19: chr18-74961397;