chr4-126549748-T-C

Position:

• chr4-126549748-T-C

Variant summary

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

The ENST00000661809.1(ENSG00000286251):​n.149-84606A>G 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 0.638 in 151,824 control chromosomes in the GnomAD database, including 31,162 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 0.64 (31162 hom., cov: 32)
• Consequence: ENST00000661809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 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
	ENST00000661809.1	n.149-84606A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96822 AN: 151706 Hom.: 31127 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.638 AC: 96909 AN: 151824 Hom.: 31162 Cov.: 32 AF XY: 0.635 AC XY: 47100 AN XY: 74186

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.644

Alfa AF: 0.646 Hom.: 15588

Bravo AF: 0.627

Asia WGS AF: 0.622 AC: 2161 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6810452; hg19: chr4-127470903;