rs7707833

Variant names:

• chr5-74992038-T-C
• rs7707833
• ENST00000505200.1:n.213-4415A>G

Variant summary

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

The ENST00000505200.1(ENSG00000249856):​n.213-4415A>G variant causes a intron 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: ENSG00000249856 ENST00000505200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 5 publications found

Genes affected

ENSG00000249856 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249856	ENST00000505200.1	n.213-4415A>G		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.753 AC: 31200 AN: 41434

American (AMR) AF: 0.425 AC: 6495 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1959 AN: 5160

South Asian (SAS) AF: 0.375 AC: 1801 AN: 4808

European-Finnish (FIN) AF: 0.420 AC: 4437 AN: 10560

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27211 AN: 67936

Other (OTH) AF: 0.460 AC: 971 AN: 2112

Alfa AF: 0.455 Hom.: 6358

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7707833; hg19: chr5-74287863;