rs1531851

chr2-20494362-T-C

Variant summary

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

The NR_157978.1(LOC107985856):n.360-5454A>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 0.321 in 152,136 control chromosomes in the GnomAD database, including 9,024 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 0.32 (9024 hom., cov: 32)
• Consequence: LOC107985856 NR_157978.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

LOC107985856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985856	NR_157978.1	n.360-5454A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48822 AN: 152018 Hom.: 9010 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.321 AC: 48870 AN: 152136 Hom.: 9024 Cov.: 32 AF XY: 0.318 AC XY: 23678 AN XY: 74384

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.312

Alfa AF: 0.286 Hom.: 1200

Bravo AF: 0.327

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.74
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531851; hg19: chr2-20694122;