rs7720838

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 51 publications found

Genes affected

ENSG00000285616 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.463 AC: 19161 AN: 41414

American (AMR) AF: 0.491 AC: 7481 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1811 AN: 3466

East Asian (EAS) AF: 0.185 AC: 955 AN: 5152

South Asian (SAS) AF: 0.247 AC: 1187 AN: 4814

European-Finnish (FIN) AF: 0.494 AC: 5204 AN: 10544

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39510 AN: 67918

Other (OTH) AF: 0.498 AC: 1051 AN: 2112

Alfa AF: 0.549 Hom.: 103929

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7720838; hg19: chr5-40486896;