4-62194862-T-C

Variant summary

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

The ENST00000687436.2(ENSG00000288659):n.374-25469T>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 0.605 in 151,716 control chromosomes in the GnomAD database, including 28,201 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 (28201 hom., cov: 30)
• Consequence: ENST00000687436.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927145	XR_938809.3	n.372-25469T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687436.2	n.374-25469T>C		intron_variant, non_coding_transcript_variant
	ENST00000676649.1	n.447-25469T>C		intron_variant, non_coding_transcript_variant
	ENST00000702460.1	n.277-19787T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91718 AN: 151596 Hom.: 28158 Cov.: 30

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.605 AC: 91821 AN: 151716 Hom.: 28201 Cov.: 30 AF XY: 0.603 AC XY: 44662 AN XY: 74126

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.619

Alfa AF: 0.576 Hom.: 24698

Bravo AF: 0.615

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4446347; hg19: chr4-63060580;