rs1510716

chr4-28528216-T-C

Variant summary

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

The ENST00000509416.1(ENSG00000250064):n.403-49700T>C 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 0.317 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: ENST00000509416.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374557	XR_001741640.2	n.891-49700T>C		intron_variant, non_coding_transcript_variant
LOC105374558	XR_925528.3	n.332-5060A>G		intron_variant, non_coding_transcript_variant
LOC105374557	XR_001741639.2	n.301-49700T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000509416.1	n.403-49700T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.325

Alfa AF: 0.318 Hom.: 3755

Bravo AF: 0.321

Asia WGS AF: 0.562 AC: 1952 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1510716; hg19: chr4-28529838;