rs9965495

Positions:

• chr18-60366443-G-A

Variant summary

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

The ENST00000658928.1(ENSG00000285681):​n.156+37098G>A 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 0.36 in 151,966 control chromosomes in the GnomAD database, including 10,920 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 0.36 (10920 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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
	ENST00000658928.1	n.156+37098G>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+37098G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54641 AN: 151848 Hom.: 10904 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.360 AC: 54692 AN: 151966 Hom.: 10920 Cov.: 32 AF XY: 0.351 AC XY: 26092 AN XY: 74264

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.340

Alfa AF: 0.340 Hom.: 1186

Bravo AF: 0.375

Asia WGS AF: 0.230 AC: 801 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	0.50
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9965495; hg19: chr18-58033676;