rs268091

Variant names:

• chr5-39506521-G-C
• rs268091
• ENST00000767352.1:n.74C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-39506521-G-C
• chr5-39506521-G-T

Variant summary

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

The ENST00000767352.1(ENSG00000299909):​n.74C>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 0.361 in 151,992 control chromosomes in the GnomAD database, including 10,531 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 0.36 (10531 hom., cov: 32)
• Consequence: ENSG00000299909 ENST00000767352.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 3 publications found

Genes affected

ENSG00000299909 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 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
ENSG00000299909	ENST00000767352.1	n.74C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54816 AN: 151874 Hom.: 10536 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.361 AC: 54832 AN: 151992 Hom.: 10531 Cov.: 32 AF XY: 0.367 AC XY: 27251 AN XY: 74268

African (AFR) AF: 0.257 AC: 10669 AN: 41466

American (AMR) AF: 0.273 AC: 4175 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2425 AN: 5140

South Asian (SAS) AF: 0.390 AC: 1873 AN: 4804

European-Finnish (FIN) AF: 0.539 AC: 5698 AN: 10572

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27485 AN: 67952

Other (OTH) AF: 0.348 AC: 735 AN: 2112

Alfa AF: 0.385 Hom.: 1477

Bravo AF: 0.335

Asia WGS AF: 0.421 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs268091; hg19: chr5-39506623;