12-4991081-G-T

Position:

• chr12-4991081-G-T

Variant summary

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

The ENST00000640877.1(ENSG00000256654):​n.694-3232G>T 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 0.456 in 151,996 control chromosomes in the GnomAD database, including 16,176 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 0.46 (16176 hom., cov: 32)
• Consequence: ENST00000640877.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000640877.1	n.694-3232G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69203 AN: 151878 Hom.: 16153 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.456 AC: 69282 AN: 151996 Hom.: 16176 Cov.: 32 AF XY: 0.453 AC XY: 33646 AN XY: 74270

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.469

Alfa AF: 0.475 Hom.: 12892

Bravo AF: 0.438

Asia WGS AF: 0.434 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.051
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1014665; hg19: chr12-5100247;