7-57639445-C-T

Variant summary

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

The ENST00000511350.2(ENSG00000243981):n.52-2235G>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 0.707 in 151,408 control chromosomes in the GnomAD database, including 38,548 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 0.71 (38548 hom., cov: 30)
• Consequence: ENST00000511350.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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
	ENST00000511350.2	n.52-2235G>A		intron_variant, non_coding_transcript_variant
	ENST00000605139.1	n.417-2235G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.707 AC: 106937 AN: 151292 Hom.: 38537 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.707 AC: 106987 AN: 151408 Hom.: 38548 Cov.: 30 AF XY: 0.702 AC XY: 51921 AN XY: 73986

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.716

Alfa AF: 0.734 Hom.: 13731

Bravo AF: 0.708

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4870684; hg19: chr7-57699151; COSMIC: COSV71413610;