rs744056

Positions:

• chr6-6733307-A-G

Variant summary

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

The XR_001743949.2(LOC101928047):​n.5418A>G 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 0.582 in 151,816 control chromosomes in the GnomAD database, including 26,452 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 0.58 (26452 hom., cov: 31)
• Consequence: LOC101928047 XR_001743949.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

Genes affected

LOC101928047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928047	XR_001743949.2	n.5418A>G		non_coding_transcript_exon_variant	6/6
LOC101928004	XR_007059429.1	n.486-21449T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689004.1	n.563+11630T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88353 AN: 151700 Hom.: 26447 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.582 AC: 88379 AN: 151816 Hom.: 26452 Cov.: 31 AF XY: 0.573 AC XY: 42539 AN XY: 74214

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.557

Alfa AF: 0.599 Hom.: 3428

Bravo AF: 0.576

Asia WGS AF: 0.294 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs744056; hg19: chr6-6733540;