rs10515982

Positions:

• chr18-60757156-A-G
• chr18-60757156-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655645.1(ENSG00000267098):​n.111+14780T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 151,788 control chromosomes in the GnomAD database, including 713 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 0.061 (713 hom., cov: 31)
• Consequence: ENST00000655645.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655645.1	n.111+14780T>C		intron_variant, non_coding_transcript_variant
	ENST00000591869.1	n.175+14780T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9225 AN: 151672 Hom.: 703 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.0222

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0605

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

GnomAD4 genome AF: 0.0611 AC: 9269 AN: 151788 Hom.: 713 Cov.: 31 AF XY: 0.0596 AC XY: 4420 AN XY: 74210

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0393

Gnomad4 ASJ AF: 0.0168

Gnomad4 EAS AF: 0.0223

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.00274

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.00945 Hom.: 7

Bravo AF: 0.0701

Asia WGS AF: 0.0340 AC: 119 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	0.18
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515982; hg19: chr18-58424389;