chr6-63443786-G-A

Position:

• chr6-63443786-G-A

Variant summary

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

The ENST00000701584.1(ENSG00000289911):​n.134-28C>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 0.582 in 151,880 control chromosomes in the GnomAD database, including 25,976 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 0.58 (25976 hom., cov: 30)
• Consequence: ENST00000701584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

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 (SAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGSN	XM_047418866.1	c.-963-28C>T		intron_variant			XP_047274822.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701584.1	n.134-28C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88332 AN: 151762 Hom.: 25965 Cov.: 30

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.582 AC: 88386 AN: 151880 Hom.: 25976 Cov.: 30 AF XY: 0.586 AC XY: 43497 AN XY: 74228

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.598

Alfa AF: 0.575 Hom.: 3107

Bravo AF: 0.571

Asia WGS AF: 0.634 AC: 2206 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	1.7
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2076874; hg19: chr6-64153691;