rs4719814

chr7-25461637-G-A

Variant summary

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

The ENST00000650415.1(ENSG00000285960):n.67-20147G>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 0.642 in 151,972 control chromosomes in the GnomAD database, including 32,171 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 0.64 (32171 hom., cov: 32)
• Consequence: ENST00000650415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

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 (AFR) allele frequency at 95% confidence interval = 0.691 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
	ENST00000650415.1	n.67-20147G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97462 AN: 151854 Hom.: 32123 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.642 AC: 97569 AN: 151972 Hom.: 32171 Cov.: 32 AF XY: 0.635 AC XY: 47197 AN XY: 74276

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.625

Alfa AF: 0.641 Hom.: 65653

Bravo AF: 0.635

Asia WGS AF: 0.399 AC: 1388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.8
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4719814; hg19: chr7-25501256;