rs4720952

Positions:

• chr7-11251773-G-A

Variant summary

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

The ENST00000428533.5(ENSG00000230333):​n.138+54329G>A 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 0.571 in 151,846 control chromosomes in the GnomAD database, including 25,053 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 0.57 (25053 hom., cov: 32)
• Consequence: ENST00000428533.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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
	ENST00000428533.5	n.138+54329G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000428967.5	n.497+3398G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000441110.5	n.546+7294G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000599875.1	n.186+24118G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86549 AN: 151728 Hom.: 25018 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.571 AC: 86630 AN: 151846 Hom.: 25053 Cov.: 32 AF XY: 0.570 AC XY: 42281 AN XY: 74184

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.605

Alfa AF: 0.549 Hom.: 42274

Bravo AF: 0.577

Asia WGS AF: 0.516 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4720952; hg19: chr7-11291400;