rs7700504

Variant names:

• chr5-74015515-A-G
• rs7700504
• ENST00000803880.1:n.704-26561A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-74015515-A-G
• chr5-74015515-A-T

Variant summary

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

The ENST00000803880.1(ENSG00000304504):​n.704-26561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,012 control chromosomes in the GnomAD database, including 18,931 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 0.45 (18931 hom., cov: 32)
• Consequence: ENSG00000304504 ENST00000803880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 1 publications found

Genes affected

ENSG00000304504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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
ENSG00000304504	ENST00000803880.1	n.704-26561A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68542 AN: 151894 Hom.: 18876 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.452 AC: 68654 AN: 152012 Hom.: 18931 Cov.: 32 AF XY: 0.451 AC XY: 33505 AN XY: 74296

African (AFR) AF: 0.774 AC: 32094 AN: 41440

American (AMR) AF: 0.479 AC: 7313 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2666 AN: 5162

South Asian (SAS) AF: 0.344 AC: 1653 AN: 4810

European-Finnish (FIN) AF: 0.270 AC: 2854 AN: 10566

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19536 AN: 67976

Other (OTH) AF: 0.437 AC: 921 AN: 2108

Alfa AF: 0.382 Hom.: 5360

Bravo AF: 0.485

Asia WGS AF: 0.439 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.88
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7700504; hg19: chr5-73311340;