rs4731413

Positions:

• chr7-128196079-G-A

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-9610G>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 0.141 in 152,152 control chromosomes in the GnomAD database, including 1,952 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 0.14 (1952 hom., cov: 32)
• Consequence: ENST00000710955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710955.1	n.306-9610G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21525 AN: 152034 Hom.: 1952 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.141 AC: 21522 AN: 152152 Hom.: 1952 Cov.: 32 AF XY: 0.135 AC XY: 10069 AN XY: 74374

Gnomad4 AFR AF: 0.0401

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0310

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.174

Alfa AF: 0.179 Hom.: 731

Bravo AF: 0.139

Asia WGS AF: 0.0730 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731413; hg19: chr7-127836132;