rs10485660

Positions:

• chr20-39763637-A-G

Variant summary

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

The ENST00000668185.1(ENSG00000229976):​n.280-318A>G 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 0.0872 in 152,104 control chromosomes in the GnomAD database, including 1,233 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 0.087 (1233 hom., cov: 32)
• Consequence: ENST00000668185.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372614	XR_936714.3	n.280-318A>G		intron_variant, non_coding_transcript_variant
LOC105372614	XR_001754592.2	n.226-1951A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668185.1	n.280-318A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13218 AN: 151988 Hom.: 1222 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00834

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0872 AC: 13268 AN: 152104 Hom.: 1233 Cov.: 32 AF XY: 0.0906 AC XY: 6736 AN XY: 74352

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.00835

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0504 Hom.: 72

Bravo AF: 0.104

Asia WGS AF: 0.195 AC: 677 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.16
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485660; hg19: chr20-38392279;