rs1510716

Variant names:

• chr4-28528216-T-C
• rs1510716
• ENST00000509416.1:n.403-49700T>C

Variant summary

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

The ENST00000509416.1(ENSG00000250064):​n.403-49700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,836 control chromosomes in the GnomAD database, including 8,574 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 (8574 hom., cov: 32)
• Consequence: ENSG00000250064 ENST00000509416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 0 publications found

Genes affected

ENSG00000250064 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509416.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374557	NR_188396.1		n.348-49700T>C		intron	N/A
	LOC105374557	NR_188397.1		n.347+51707T>C		intron	N/A
	LOC105374557	NR_188399.1		n.300+51707T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250064	ENST00000509416.1	TSL:3	n.403-49700T>C		intron	N/A
	ENSG00000250064	ENST00000729962.1		n.219-49700T>C		intron	N/A
	ENSG00000250064	ENST00000729963.1		n.211-24159T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48091 AN: 151716 Hom.: 8564 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.317 AC: 48120 AN: 151836 Hom.: 8574 Cov.: 32 AF XY: 0.323 AC XY: 23965 AN XY: 74238

African (AFR) AF: 0.205 AC: 8485 AN: 41460

American (AMR) AF: 0.430 AC: 6544 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3466

East Asian (EAS) AF: 0.781 AC: 4029 AN: 5162

South Asian (SAS) AF: 0.424 AC: 2043 AN: 4822

European-Finnish (FIN) AF: 0.338 AC: 3558 AN: 10542

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21312 AN: 67872

Other (OTH) AF: 0.325 AC: 683 AN: 2102

Alfa AF: 0.316 Hom.: 4182

Bravo AF: 0.321

Asia WGS AF: 0.562 AC: 1952 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs1510716; hg19: chr4-28529838;