6-1548134-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607350.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272279	ENST00000607350.2	TSL:6	n.128+6998T>C		intron	N/A
	ENSG00000272279	ENST00000808963.1		n.223+947T>C		intron	N/A
	ENSG00000272279	ENST00000808964.1		n.210+947T>C		intron	N/A

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 v4.9

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;