rs1531851

Variant names:

• chr2-20494362-T-C
• rs1531851
• ENST00000448241.2:n.309-3422T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448241.2(ENSG00000228950):​n.309-3422T>C variant causes a intron 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: ENSG00000228950 ENST00000448241.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 3 publications found

Genes affected

ENSG00000228950 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107985856	NR_157978.1	n.360-5454A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228950	ENST00000448241.2	n.309-3422T>C		intron_variant	Intron 2 of 2	4

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

African (AFR) AF: 0.509 AC: 21093 AN: 41470

American (AMR) AF: 0.242 AC: 3698 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3472

East Asian (EAS) AF: 0.134 AC: 695 AN: 5174

South Asian (SAS) AF: 0.264 AC: 1274 AN: 4826

European-Finnish (FIN) AF: 0.255 AC: 2698 AN: 10582

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17392 AN: 68004

Other (OTH) AF: 0.312 AC: 658 AN: 2112

Alfa AF: 0.292 Hom.: 1308

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1531851; hg19: chr2-20694122;