rs7707833

chr5-74992038-T-C

Variant summary

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

The ENST00000505200.1(ENSG00000249856):n.213-4415A>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 0.501 in 151,954 control chromosomes in the GnomAD database, including 20,860 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 0.50 (20860 hom., cov: 31)
• Consequence: ENST00000505200.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000505200.1	n.213-4415A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75945 AN: 151836 Hom.: 20814 Cov.: 31

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.501 AC: 76055 AN: 151954 Hom.: 20860 Cov.: 31 AF XY: 0.497 AC XY: 36940 AN XY: 74276

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.460

Alfa AF: 0.450 Hom.: 3453

Bravo AF: 0.515

Asia WGS AF: 0.410 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.52
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7707833; hg19: chr5-74287863;