11-35854987-G-C

Variant names:

• chr11-35854987-G-C
• rs650693
• ENST00000730437.1:n.295C>G

Variant summary

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

The ENST00000730437.1(ENSG00000254919):​n.295C>G 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 0.531 in 151,864 control chromosomes in the GnomAD database, including 22,349 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 0.53 (22349 hom., cov: 30)
• Consequence: ENSG00000254919 ENST00000730437.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 0 publications found

Genes affected

ENSG00000254919 (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 (AMR) allele frequency at 95% confidence interval = 0.604 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
ENSG00000254919	ENST00000730437.1	n.295C>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000254919	ENST00000730429.1	n.264+63024C>G		intron_variant	Intron 2 of 3
ENSG00000254919	ENST00000730430.1	n.268+63024C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80542 AN: 151746 Hom.: 22336 Cov.: 30

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.531 AC: 80578 AN: 151864 Hom.: 22349 Cov.: 30 AF XY: 0.530 AC XY: 39356 AN XY: 74220

African (AFR) AF: 0.367 AC: 15178 AN: 41394

American (AMR) AF: 0.615 AC: 9378 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2327 AN: 5156

South Asian (SAS) AF: 0.473 AC: 2267 AN: 4796

European-Finnish (FIN) AF: 0.625 AC: 6599 AN: 10564

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40987 AN: 67918

Other (OTH) AF: 0.536 AC: 1133 AN: 2112

Alfa AF: 0.433 Hom.: 1233

Bravo AF: 0.526

Asia WGS AF: 0.458 AC: 1595 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	2.4
DANN	Benign	0.51
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs650693; hg19: chr11-35876537;