rs7700506

Variant names:

• chr5-56700771-A-G
• rs7700506
• ENST00000821819.1:n.62-24243T>C

Variant summary

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

The ENST00000821819.1(ENSG00000306891):​n.62-24243T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,968 control chromosomes in the GnomAD database, including 29,044 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 0.61 (29044 hom., cov: 31)
• Consequence: ENSG00000306891 ENST00000821819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.71
• Publications: 2 publications found

Genes affected

ENSG00000306891 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 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
ENSG00000306891	ENST00000821819.1	n.62-24243T>C		intron_variant	Intron 1 of 4
ENSG00000306891	ENST00000821820.1	n.94-18117T>C		intron_variant	Intron 1 of 2
ENSG00000306891	ENST00000821821.1	n.144-513T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93145 AN: 151850 Hom.: 29017 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.613 AC: 93217 AN: 151968 Hom.: 29044 Cov.: 31 AF XY: 0.604 AC XY: 44850 AN XY: 74296

African (AFR) AF: 0.622 AC: 25759 AN: 41420

American (AMR) AF: 0.614 AC: 9366 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2274 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1615 AN: 5146

South Asian (SAS) AF: 0.471 AC: 2272 AN: 4822

European-Finnish (FIN) AF: 0.544 AC: 5743 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44250 AN: 67982

Other (OTH) AF: 0.611 AC: 1289 AN: 2108

Alfa AF: 0.635 Hom.: 17306

Bravo AF: 0.622

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.34
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs7700506; hg19: chr5-55996598; COSMIC: COSV56538847;