chr10-10215050-C-T

Variant names:

• chr10-10215050-C-T
• rs11256534
• ENST00000738164.1:n.300-71784C>T

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.300-71784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0563 in 152,194 control chromosomes in the GnomAD database, including 336 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 0.056 (336 hom., cov: 32)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 2 publications found

Genes affected

ENSG00000296323 (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 (NFE) allele frequency at 95% confidence interval = 0.0808 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
ENSG00000296323	ENST00000738164.1	n.300-71784C>T		intron_variant	Intron 3 of 8
ENSG00000296323	ENST00000738165.1	n.327-71784C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8568 AN: 152076 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0563 AC: 8563 AN: 152194 Hom.: 336 Cov.: 32 AF XY: 0.0561 AC XY: 4173 AN XY: 74388

African (AFR) AF: 0.0146 AC: 607 AN: 41544

American (AMR) AF: 0.0450 AC: 687 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3470

East Asian (EAS) AF: 0.0304 AC: 157 AN: 5160

South Asian (SAS) AF: 0.0520 AC: 251 AN: 4824

European-Finnish (FIN) AF: 0.0755 AC: 800 AN: 10600

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0826 AC: 5615 AN: 68014

Other (OTH) AF: 0.0461 AC: 97 AN: 2104

Alfa AF: 0.0754 Hom.: 272

Bravo AF: 0.0522

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.77
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11256534; hg19: chr10-10257013;