20-40633339-G-A

Position:

• chr20-40633339-G-A

Variant summary

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

The XR_001754596.2(LOC102724968):​n.243+2249C>T 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 0.378 in 152,108 control chromosomes in the GnomAD database, including 11,046 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 0.38 (11046 hom., cov: 33)
• Consequence: LOC102724968 XR_001754596.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

Genes affected

LOC102724968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724968	XR_001754596.2	n.243+2249C>T		intron_variant, non_coding_transcript_variant
LOC102724968	XR_001754597.1	n.180+10572C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57468 AN: 151990 Hom.: 11055 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.378 AC: 57467 AN: 152108 Hom.: 11046 Cov.: 33 AF XY: 0.381 AC XY: 28312 AN XY: 74350

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.365

Alfa AF: 0.398 Hom.: 5667

Bravo AF: 0.372

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6065259; hg19: chr20-39261979;