rs700752

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

Genes affected

ENSG00000233539 (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 (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487094.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233539	ENST00000469937.2	TSL:5	n.104-20986G>C		intron	N/A
	ENSG00000233539	ENST00000487094.1	TSL:3	n.111-35180G>C		intron	N/A

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

African (AFR) AF: 0.623 AC: 25832 AN: 41470

American (AMR) AF: 0.561 AC: 8578 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2281 AN: 3468

East Asian (EAS) AF: 0.854 AC: 4394 AN: 5144

South Asian (SAS) AF: 0.715 AC: 3453 AN: 4830

European-Finnish (FIN) AF: 0.734 AC: 7763 AN: 10576

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44155 AN: 67970

Other (OTH) AF: 0.641 AC: 1356 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.39
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs700752; hg19: chr7-46753553;