rs7720838

Variant names:

• chr5-40486794-G-T
• rs7720838
• ENST00000648975.1:n.2420+1217C>A

Variant summary

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

The ENST00000648975.1(ENSG00000285616):​n.2420+1217C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,870 control chromosomes in the GnomAD database, including 20,417 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 0.51 (20417 hom., cov: 31)
• Consequence: ENSG00000285616 ENST00000648975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

ENSG00000285616 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 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
ENSG00000285616	ENST00000648975.1	n.2420+1217C>A		intron_variant	Intron 1 of 2
ENSG00000285552	ENST00000649444.1	n.242+296G>T		intron_variant	Intron 2 of 2
ENSG00000285552	ENST00000649894.1	n.120-17077G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77124 AN: 151752 Hom.: 20399 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.508 AC: 77175 AN: 151870 Hom.: 20417 Cov.: 31 AF XY: 0.498 AC XY: 36920 AN XY: 74210

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.498

Alfa AF: 0.556 Hom.: 49553

Bravo AF: 0.510

Asia WGS AF: 0.236 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7720838; hg19: chr5-40486896;