chr6-140823507-G-A

Variant names:

• chr6-140823507-G-A
• rs659647
• XR_428030.5:n.23141C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LOC102723724 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC102723724	XR_428030.5	n.23141C>T		non_coding_transcript_exon_variant	Exon 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234147	ENST00000650553.2	n.195-7277C>T		intron_variant	Intron 1 of 4
ENSG00000234147	ENST00000692940.2	n.158-7277C>T		intron_variant	Intron 2 of 2
ENSG00000234147	ENST00000700918.1	n.243-7277C>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.461 AC: 19074 AN: 41380

American (AMR) AF: 0.664 AC: 10140 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3459 AN: 5132

South Asian (SAS) AF: 0.692 AC: 3335 AN: 4818

European-Finnish (FIN) AF: 0.638 AC: 6738 AN: 10566

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45659 AN: 67958

Other (OTH) AF: 0.606 AC: 1277 AN: 2106

Alfa AF: 0.642 Hom.: 4152

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

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