chr6-1548134-A-G

Variant names:

• chr6-1548134-A-G
• rs2745572
• XR_001743922.2:n.1339T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001743922.2(LOC102723944):​n.1339T>C 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 0.32 in 151,970 control chromosomes in the GnomAD database, including 8,510 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 0.32 (8510 hom., cov: 31)
• Consequence: LOC102723944 XR_001743922.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943
• Publications: 29 publications found

Genes affected

LOC102723944 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723944	XR_001743922.2	n.1339T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC102723944	XR_001743921.2	n.294+4212T>C		intron_variant	Intron 2 of 2
LOC102723944	XR_427861.4	n.234+4212T>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272279	ENST00000607350.2	n.128+6998T>C		intron_variant	Intron 1 of 1	6
ENSG00000272279	ENST00000808963.1	n.223+947T>C		intron_variant	Intron 2 of 2
ENSG00000272279	ENST00000808964.1	n.210+947T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48542 AN: 151850 Hom.: 8504 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.320 AC: 48556 AN: 151970 Hom.: 8510 Cov.: 31 AF XY: 0.329 AC XY: 24451 AN XY: 74282

African (AFR) AF: 0.174 AC: 7211 AN: 41460

American (AMR) AF: 0.395 AC: 6035 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2433 AN: 5142

South Asian (SAS) AF: 0.457 AC: 2204 AN: 4822

European-Finnish (FIN) AF: 0.428 AC: 4517 AN: 10562

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23604 AN: 67934

Other (OTH) AF: 0.364 AC: 768 AN: 2112

Alfa AF: 0.342 Hom.: 5726

Bravo AF: 0.310

Asia WGS AF: 0.481 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs2745572; hg19: chr6-1548369;