rs659647

chr6-140823507-G-Achr6-140823507-G-T

Variant summary

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

The XR_428030.5(LOC102723724):n.23141C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,892 control chromosomes in the GnomAD database, including 29,204 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 0.61 (29204 hom., cov: 31)
• Consequence: LOC102723724 XR_428030.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

Genes affected

LOC102723724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723724	XR_428030.5	n.23141C>T		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650553.2	n.195-7277C>T		intron_variant, non_coding_transcript_variant
	ENST00000692940.1	n.152-7277C>T		intron_variant, non_coding_transcript_variant
	ENST00000700918.1	n.243-7277C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92843 AN: 151774 Hom.: 29199 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.611 AC: 92881 AN: 151892 Hom.: 29204 Cov.: 31 AF XY: 0.613 AC XY: 45541 AN XY: 74232

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.606

Alfa AF: 0.649 Hom.: 4066

Bravo AF: 0.603

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.82
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs659647; hg19: chr6-141144644; COSMIC: COSV69429096;