ENST00000728740.1:n.210-10965C>T

Variant names:

• chr6-1573378-G-A
• rs2338
• ENST00000728740.1:n.210-10965C>T

Variant summary

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

The ENST00000728740.1(ENSG00000295230):​n.210-10965C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,134 control chromosomes in the GnomAD database, including 6,709 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 0.29 (6709 hom., cov: 33)
• Consequence: ENSG00000295230 ENST00000728740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 16 publications found

Genes affected

ENSG00000295230 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 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
ENSG00000295230	ENST00000728740.1	n.210-10965C>T		intron_variant	Intron 1 of 4
ENSG00000295230	ENST00000728741.1	n.210-10965C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43938 AN: 152020 Hom.: 6701 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.289 AC: 43975 AN: 152134 Hom.: 6709 Cov.: 33 AF XY: 0.294 AC XY: 21894 AN XY: 74386

African (AFR) AF: 0.236 AC: 9791 AN: 41488

American (AMR) AF: 0.445 AC: 6812 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1588 AN: 5166

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4828

European-Finnish (FIN) AF: 0.313 AC: 3311 AN: 10578

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18772 AN: 67996

Other (OTH) AF: 0.341 AC: 720 AN: 2112

Alfa AF: 0.288 Hom.: 18575

Bravo AF: 0.299

Asia WGS AF: 0.329 AC: 1140 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2338; hg19: chr6-1573613;