rs230014

chr20-51123323-G-A

Variant summary

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

The XR_001754668.2(LOC105372662):n.85-544C>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 0.569 in 152,018 control chromosomes in the GnomAD database, including 26,325 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 0.57 (26325 hom., cov: 32)
• Consequence: LOC105372662 XR_001754668.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

LOC105372662 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372662	XR_001754668.2	n.85-544C>T		intron_variant, non_coding_transcript_variant
LOC105372661	XR_007067649.1	n.89+5845G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86445 AN: 151900 Hom.: 26264 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.569 AC: 86565 AN: 152018 Hom.: 26325 Cov.: 32 AF XY: 0.566 AC XY: 42020 AN XY: 74298

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.552

Alfa AF: 0.511 Hom.: 7942

Bravo AF: 0.575

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.96
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230014; hg19: chr20-49739860;