rs1563796

chr4-62202277-T-Cchr4-62202277-T-G

Variant summary

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

The ENST00000687436.2(ENSG00000288659):n.374-18054T>C 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 0.613 in 151,930 control chromosomes in the GnomAD database, including 29,571 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 0.61 (29571 hom., cov: 31)
• Consequence: ENST00000687436.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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 = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927145	XR_938809.3	n.372-18054T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687436.2	n.374-18054T>C		intron_variant, non_coding_transcript_variant
	ENST00000676649.1	n.447-18054T>C		intron_variant, non_coding_transcript_variant
	ENST00000702460.1	n.277-12372T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93055 AN: 151812 Hom.: 29560 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.613 AC: 93094 AN: 151930 Hom.: 29571 Cov.: 31 AF XY: 0.613 AC XY: 45530 AN XY: 74280

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.600

Alfa AF: 0.679 Hom.: 59236

Bravo AF: 0.600

Asia WGS AF: 0.508 AC: 1767 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
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: rs1563796; hg19: chr4-63067995;