rs2008645

Positions:

• chr20-48396747-G-A

Variant summary

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

The XR_936812.3(LOC105372643):​n.1194+392G>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 0.536 in 152,062 control chromosomes in the GnomAD database, including 23,885 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 0.54 (23885 hom., cov: 32)
• Consequence: LOC105372643 XR_936812.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

LOC105372643 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372643	XR_936812.3	n.1194+392G>A		intron_variant, non_coding_transcript_variant
LOC105372643	XR_001754655.2	n.1194+392G>A		intron_variant, non_coding_transcript_variant
LOC105372643	XR_007067635.1	n.981+392G>A		intron_variant, non_coding_transcript_variant
LOC105372643	XR_007067636.1	n.981+392G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81423 AN: 151944 Hom.: 23841 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.536 AC: 81536 AN: 152062 Hom.: 23885 Cov.: 32 AF XY: 0.527 AC XY: 39196 AN XY: 74330

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.517

Alfa AF: 0.460 Hom.: 3535

Bravo AF: 0.575

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2008645; hg19: chr20-47025490;