rs114846327

Variant names:

• chr5-36436477-A-G
• rs114846327
• ENST00000765258.1:n.133-6763A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000765258.1(ENSG00000299633):​n.133-6763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 152,286 control chromosomes in the GnomAD database, including 38 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 0.019 (38 hom., cov: 32)
• Consequence: ENSG00000299633 ENST00000765258.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 4 publications found

Genes affected

ENSG00000299633 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0187 (2844/152286) while in subpopulation NFE AF = 0.0311 (2113/68010). AF 95% confidence interval is 0.03. There are 38 homozygotes in GnomAd4. There are 1351 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 38 gene

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
ENSG00000299633	ENST00000765258.1	n.133-6763A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 2845 AN: 152168 Hom.: 38 Cov.: 32

Gnomad AFR AF: 0.00521

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0311

Gnomad OTH AF: 0.00955

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

GnomAD4 genome AF: 0.0187 AC: 2844 AN: 152286 Hom.: 38 Cov.: 32 AF XY: 0.0181 AC XY: 1351 AN XY: 74460

African (AFR) AF: 0.00520 AC: 216 AN: 41566

American (AMR) AF: 0.0107 AC: 163 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00311 AC: 15 AN: 4818

European-Finnish (FIN) AF: 0.0274 AC: 291 AN: 10616

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0311 AC: 2113 AN: 68010

Other (OTH) AF: 0.00945 AC: 20 AN: 2116

Alfa AF: 0.0286 Hom.: 112

Bravo AF: 0.0167

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.67
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs114846327; hg19: chr5-36436579;