rs4947882

chr7-54190442-G-T

Variant summary

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

The ENST00000657889.1(ENSG00000287953):n.323-3651C>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 0.841 in 151,956 control chromosomes in the GnomAD database, including 55,951 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 0.84 (55951 hom., cov: 32)
• Consequence: ENST00000657889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 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
	ENST00000657889.1	n.323-3651C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127692 AN: 151840 Hom.: 55933 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.841 AC: 127743 AN: 151956 Hom.: 55951 Cov.: 32 AF XY: 0.839 AC XY: 62354 AN XY: 74280

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.876

Alfa AF: 0.894 Hom.: 7749

Bravo AF: 0.827

Asia WGS AF: 0.827 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.34
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4947882; hg19: chr7-54258135;