chr20-40642176-C-T

Position:

• chr20-40642176-C-T

Variant summary

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

The XR_001754597.1(LOC102724968):​n.180+1735G>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 0.361 in 152,160 control chromosomes in the GnomAD database, including 10,239 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 (10239 hom., cov: 33)
• Consequence: LOC102724968 XR_001754597.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

Genes affected

LOC102724968 (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 = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724968	XR_001754597.1	n.180+1735G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54965 AN: 152042 Hom.: 10247 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.361 AC: 54963 AN: 152160 Hom.: 10239 Cov.: 33 AF XY: 0.365 AC XY: 27124 AN XY: 74386

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.357

Alfa AF: 0.366 Hom.: 5021

Bravo AF: 0.355

Asia WGS AF: 0.364 AC: 1270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11696257; hg19: chr20-39270816;