rs11042978

Variant names:

• chr11-2177188-G-T
• rs11042978
• ENST00000729780.1:n.202+1873C>A

Variant summary

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

The ENST00000729780.1(ENSG00000295395):​n.202+1873C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,220 control chromosomes in the GnomAD database, including 16,214 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 0.45 (16214 hom., cov: 35)
• Consequence: ENSG00000295395 ENST00000729780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 17 publications found

Genes affected

ENSG00000295395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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
ENSG00000295395	ENST00000729780.1	n.202+1873C>A		intron_variant	Intron 1 of 2
ENSG00000295395	ENST00000729781.1	n.226+1114C>A		intron_variant	Intron 1 of 2
ENSG00000295395	ENST00000729782.1	n.195+1114C>A		intron_variant	Intron 1 of 3
ENSG00000295395	ENST00000729783.1	n.155+1114C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68470 AN: 152102 Hom.: 16216 Cov.: 35

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.450 AC: 68485 AN: 152220 Hom.: 16214 Cov.: 35 AF XY: 0.457 AC XY: 34036 AN XY: 74426

African (AFR) AF: 0.319 AC: 13259 AN: 41528

American (AMR) AF: 0.435 AC: 6656 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1796 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4071 AN: 5182

South Asian (SAS) AF: 0.642 AC: 3103 AN: 4834

European-Finnish (FIN) AF: 0.502 AC: 5324 AN: 10598

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32574 AN: 67986

Other (OTH) AF: 0.497 AC: 1051 AN: 2114

Alfa AF: 0.478 Hom.: 69576

Bravo AF: 0.440

Asia WGS AF: 0.677 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	19
DANN	Benign	0.65
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs11042978; hg19: chr11-2198418;