rs3887942

Positions:

• chr20-23996435-A-G
• chr20-23996435-A-T

Variant summary

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

The XR_001754556.3(LOC107985438):​n.651-21A>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 0.287 in 151,674 control chromosomes in the GnomAD database, including 8,022 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 0.29 (8022 hom., cov: 32)
• Consequence: LOC107985438 XR_001754556.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

Genes affected

LOC107985438 (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 (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985438	XR_001754556.3	n.651-21A>G		intron_variant, non_coding_transcript_variant
LOC107985438	XR_001754555.3	n.651-18A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43402 AN: 151556 Hom.: 7993 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.287 AC: 43469 AN: 151674 Hom.: 8022 Cov.: 32 AF XY: 0.284 AC XY: 21022 AN XY: 74090

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.261

Alfa AF: 0.206 Hom.: 3585

Bravo AF: 0.298

Asia WGS AF: 0.214 AC: 747 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	9.2
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: rs3887942; hg19: chr20-23977072;