rs4731420

Positions:

• chr7-128223242-G-C
• chr7-128223242-G-T

Variant summary

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

The ENST00000692614.2(ENSG00000289434):​n.520-1702C>G 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 0.193 in 152,074 control chromosomes in the GnomAD database, including 2,884 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 0.19 (2884 hom., cov: 31)
• Consequence: ENST00000692614.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

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 (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901744	XR_007060516.1	n.781-791G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692614.2	n.520-1702C>G		intron_variant, non_coding_transcript_variant
	ENST00000710955.1	n.836-791G>C		intron_variant, non_coding_transcript_variant
	ENST00000690022.1	n.244-1702C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29354 AN: 151956 Hom.: 2884 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.193 AC: 29364 AN: 152074 Hom.: 2884 Cov.: 31 AF XY: 0.191 AC XY: 14231 AN XY: 74350

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.200

Alfa AF: 0.113 Hom.: 185

Bravo AF: 0.195

Asia WGS AF: 0.121 AC: 422 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	6.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731420; hg19: chr7-127863295;