rs1744140

Positions:

• chr6-63502926-T-C

Variant summary

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

The ENST00000701584.1(ENSG00000289911):​n.134-59168A>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 0.536 in 152,092 control chromosomes in the GnomAD database, including 23,658 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 0.54 (23658 hom., cov: 33)
• Consequence: ENST00000701584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

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 (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGSN	XM_047418866.1	c.-963-59168A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701584.1	n.134-59168A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81357 AN: 151974 Hom.: 23600 Cov.: 33

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.536 AC: 81483 AN: 152092 Hom.: 23658 Cov.: 33 AF XY: 0.532 AC XY: 39554 AN XY: 74360

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.494

Alfa AF: 0.455 Hom.: 12258

Bravo AF: 0.557

Asia WGS AF: 0.455 AC: 1578 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1744140; hg19: chr6-64212831;