6-1548134-A-G

Position:

• chr6-1548134-A-G

Variant summary

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

The XR_427861.4(LOC102723944):​n.234+4212T>C 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 0.32 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_427861.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943

Genes affected

LOC102723944 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC102723944	XR_427861.4	n.234+4212T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.364

Alfa AF: 0.339 Hom.: 2721

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2745572; hg19: chr6-1548369;