ENST00000775236.1:n.68-48627C>A

Variant names:

• chr5-82490877-C-A
• rs1501656
• ENST00000775236.1:n.68-48627C>A

Variant summary

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

The ENST00000775236.1(ENSG00000300956):​n.68-48627C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,046 control chromosomes in the GnomAD database, including 35,228 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 0.67 (35228 hom., cov: 31)
• Consequence: ENSG00000300956 ENST00000775236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 4 publications found

Genes affected

ENSG00000300956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 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
ENSG00000300956	ENST00000775236.1	n.68-48627C>A		intron_variant	Intron 1 of 2
ENSG00000300956	ENST00000775237.1	n.44-31945C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101417 AN: 151928 Hom.: 35184 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.668 AC: 101514 AN: 152046 Hom.: 35228 Cov.: 31 AF XY: 0.656 AC XY: 48714 AN XY: 74308

African (AFR) AF: 0.822 AC: 34109 AN: 41492

American (AMR) AF: 0.532 AC: 8123 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2319 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1659 AN: 5164

South Asian (SAS) AF: 0.443 AC: 2136 AN: 4820

European-Finnish (FIN) AF: 0.548 AC: 5793 AN: 10568

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45144 AN: 67956

Other (OTH) AF: 0.639 AC: 1348 AN: 2108

Alfa AF: 0.668 Hom.: 4958

Bravo AF: 0.675

Asia WGS AF: 0.376 AC: 1308 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.70
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1501656; hg19: chr5-81786696;