rs1681957

Positions:

• chr6-63513240-T-C

Variant summary

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

The ENST00000701584.1(ENSG00000289911):​n.133+52858A>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 152,018 control chromosomes in the GnomAD database, including 23,631 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 (23631 hom., cov: 32)
• Consequence: ENST00000701584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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.-964+52262A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701584.1	n.133+52858A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81286 AN: 151898 Hom.: 23572 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.458

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: 81414 AN: 152018 Hom.: 23631 Cov.: 32 AF XY: 0.532 AC XY: 39493 AN XY: 74298

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.495

Alfa AF: 0.492 Hom.: 3177

Bravo AF: 0.557

Asia WGS AF: 0.449 AC: 1560 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	0.23
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1681957; hg19: chr6-64223145; COSMIC: COSV63777655;