chr10-64758502-C-T

Variant names:

• chr10-64758502-C-T
• rs16920334
• ENST00000718642.1:n.149+18655C>T

Variant summary

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

The ENST00000718642.1(ENSG00000293732):​n.149+18655C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 152,024 control chromosomes in the GnomAD database, including 214 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 0.039 (214 hom., cov: 32)
• Consequence: ENSG00000293732 ENST00000718642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 1 publications found

Genes affected

ENSG00000293732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984239	XR_001747475.2	n.235+8530C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293732	ENST00000718642.1	n.149+18655C>T		intron_variant	Intron 1 of 6
ENSG00000293732	ENST00000718643.1	n.209+8530C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5903 AN: 151906 Hom.: 213 Cov.: 32

Gnomad AFR AF: 0.00679

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0585

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0374

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0389 AC: 5918 AN: 152024 Hom.: 214 Cov.: 32 AF XY: 0.0425 AC XY: 3157 AN XY: 74292

African (AFR) AF: 0.00677 AC: 281 AN: 41480

American (AMR) AF: 0.0589 AC: 898 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3468

East Asian (EAS) AF: 0.152 AC: 785 AN: 5168

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4824

European-Finnish (FIN) AF: 0.0896 AC: 946 AN: 10560

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0374 AC: 2539 AN: 67970

Other (OTH) AF: 0.0422 AC: 89 AN: 2110

Alfa AF: 0.0381 Hom.: 21

Bravo AF: 0.0371

Asia WGS AF: 0.122 AC: 422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.19
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs16920334; hg19: chr10-66518259;