6-3877710-T-C

Position:

• chr6-3877710-T-C

Variant summary

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

The ENST00000648025.1(ENSG00000233068):​n.189+559T>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 0.339 in 150,584 control chromosomes in the GnomAD database, including 9,252 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 0.34 (9252 hom., cov: 26)
• Consequence: ENST00000648025.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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
	ENST00000648025.1	n.189+559T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.339 AC: 50961 AN: 150474 Hom.: 9257 Cov.: 26

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.339 AC: 50984 AN: 150584 Hom.: 9252 Cov.: 26 AF XY: 0.340 AC XY: 24987 AN XY: 73478

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.374

Alfa AF: 0.316 Hom.: 1097

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10447475; hg19: chr6-3877944;