chr3-26368538-A-G

Variant names:

• chr3-26368538-A-G
• rs10510573
• ENST00000770754.1:n.62-79T>C

Variant summary

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

The ENST00000770754.1(ENSG00000300313):​n.62-79T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,048 control chromosomes in the GnomAD database, including 12,340 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 0.38 (12340 hom., cov: 32)
• Consequence: ENSG00000300313 ENST00000770754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 2 publications found

Genes affected

ENSG00000300313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 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
ENSG00000300313	ENST00000770754.1	n.62-79T>C		intron_variant	Intron 1 of 2
ENSG00000300313	ENST00000770753.1	n.-113T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58389 AN: 151928 Hom.: 12305 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.385 AC: 58469 AN: 152048 Hom.: 12340 Cov.: 32 AF XY: 0.383 AC XY: 28434 AN XY: 74296

African (AFR) AF: 0.566 AC: 23454 AN: 41464

American (AMR) AF: 0.436 AC: 6656 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5164

South Asian (SAS) AF: 0.351 AC: 1696 AN: 4826

European-Finnish (FIN) AF: 0.237 AC: 2508 AN: 10568

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20932 AN: 67982

Other (OTH) AF: 0.371 AC: 782 AN: 2110

Alfa AF: 0.333 Hom.: 38595

Bravo AF: 0.408

Asia WGS AF: 0.301 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.83
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10510573; hg19: chr3-26410029;