rs7703051

Positions:

• chr5-75329662-C-A

Variant summary

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

The ENST00000501886.2(ENSG00000247372):​n.198+5285G>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 0.385 in 151,508 control chromosomes in the GnomAD database, including 11,477 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 0.38 (11477 hom., cov: 31)
• Consequence: ENST00000501886.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589

Genes affected

(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 (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000501886.2	n.198+5285G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58282 AN: 151394 Hom.: 11471 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.385 AC: 58323 AN: 151508 Hom.: 11477 Cov.: 31 AF XY: 0.392 AC XY: 29024 AN XY: 73972

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.371

Alfa AF: 0.387 Hom.: 17358

Bravo AF: 0.373

Asia WGS AF: 0.545 AC: 1888 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7703051; hg19: chr5-74625487;