chr6-4379277-A-G

Position:

• chr6-4379277-A-G

Variant summary

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

The ENST00000642310.1(ENSG00000285424):​n.962+49106T>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 0.103 in 152,194 control chromosomes in the GnomAD database, including 951 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 0.10 (951 hom., cov: 32)
• Consequence: ENST00000642310.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472

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 (AMR) allele frequency at 95% confidence interval = 0.166 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
	ENST00000642310.1	n.962+49106T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15681 AN: 152076 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.103 AC: 15712 AN: 152194 Hom.: 951 Cov.: 32 AF XY: 0.104 AC XY: 7734 AN XY: 74394

Gnomad4 AFR AF: 0.0865

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0641

Gnomad4 FIN AF: 0.0865

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.123

Alfa AF: 0.102 Hom.: 1800

Bravo AF: 0.114

Asia WGS AF: 0.111 AC: 387 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	3.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17138114; hg19: chr6-4379511;