rs700752

Positions:

• chr7-46713955-C-G

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, non coding transcript 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: ENST00000487094.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000487094.1	n.111-35180G>C		intron_variant, non_coding_transcript_variant		3
	ENST00000469937.2	n.104-20986G>C		intron_variant, non_coding_transcript_variant		5

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;