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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904329	XR_007066422.1	n.721T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309801	ENST00000844041.1	n.276T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309801	ENST00000844042.1	n.229T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309801	ENST00000844037.1	n.162+1407T>C		intron_variant	Intron 1 of 1
ENSG00000309801	ENST00000844038.1	n.118+1360T>C		intron_variant	Intron 1 of 1

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 v4.3

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;