rs700750

Variant names:

• chr7-46713893-C-A
• rs700750
• ENST00000469937.2:n.104-20924G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-46713893-C-A
• chr7-46713893-C-G
• chr7-46713893-C-T

Variant summary

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

The ENST00000487094.1(ENSG00000233539):​n.111-35118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 151,894 control chromosomes in the GnomAD database, including 29,404 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 0.62 (29404 hom., cov: 32)
• Consequence: ENSG00000233539 ENST00000487094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

Genes affected

ENSG00000233539 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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.104-20924G>T		intron_variant	Intron 1 of 2	5
ENSG00000233539	ENST00000487094.1	n.111-35118G>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93902 AN: 151776 Hom.: 29385 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.619 AC: 93968 AN: 151894 Hom.: 29404 Cov.: 32 AF XY: 0.623 AC XY: 46248 AN XY: 74220

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.609

Alfa AF: 0.619 Hom.: 20053

Bravo AF: 0.604

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs700750; hg19: chr7-46753491;