10-27452030-C-T

Variant names:

• chr10-27452030-C-T
• rs660498
• ENST00000779634.1:n.86-13649C>T

Variant summary

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

The ENST00000779634.1(ENSG00000301548):​n.86-13649C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,986 control chromosomes in the GnomAD database, including 12,209 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 0.39 (12209 hom., cov: 32)
• Consequence: ENSG00000301548 ENST00000779634.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 6 publications found

Genes affected

ENSG00000301548 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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
ENSG00000301548	ENST00000779634.1	n.86-13649C>T		intron_variant	Intron 1 of 2
ENSG00000301548	ENST00000779635.1	n.229-9150C>T		intron_variant	Intron 2 of 2
ENSG00000301548	ENST00000779636.1	n.229-2873C>T		intron_variant	Intron 2 of 3
ENSG00000301548	ENST00000779637.1	n.187-2873C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59638 AN: 151868 Hom.: 12196 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.393 AC: 59685 AN: 151986 Hom.: 12209 Cov.: 32 AF XY: 0.382 AC XY: 28349 AN XY: 74286

African (AFR) AF: 0.459 AC: 18999 AN: 41408

American (AMR) AF: 0.361 AC: 5520 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3470

East Asian (EAS) AF: 0.0191 AC: 99 AN: 5178

South Asian (SAS) AF: 0.274 AC: 1320 AN: 4818

European-Finnish (FIN) AF: 0.329 AC: 3469 AN: 10558

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27943 AN: 67972

Other (OTH) AF: 0.378 AC: 797 AN: 2106

Alfa AF: 0.397 Hom.: 14261

Bravo AF: 0.399

Asia WGS AF: 0.177 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.57
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs660498; hg19: chr10-27740959;