rs700752

Variant names:

• chr7-46713955-C-G
• rs700752
• ENST00000469937.2:n.104-20986G>C

Variant summary

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

The ENST00000487094.1(ENSG00000233539):​n.111-35180G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,054 control chromosomes in the GnomAD database, including 32,250 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 0.65 (32250 hom., cov: 32)
• Consequence: ENSG00000233539 ENST00000487094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414

Genes affected

ENSG00000233539 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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
ENSG00000233539	ENST00000469937.2	n.104-20986G>C		intron_variant	Intron 1 of 2	5
ENSG00000233539	ENST00000487094.1	n.111-35180G>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98493 AN: 151936 Hom.: 32227 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.648 AC: 98563 AN: 152054 Hom.: 32250 Cov.: 32 AF XY: 0.652 AC XY: 48450 AN XY: 74316

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.641

Alfa AF: 0.645 Hom.: 3930

Bravo AF: 0.634

Asia WGS AF: 0.765 AC: 2662 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	3.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs700752; hg19: chr7-46753553;