rs1357056

Positions:

• chr6-122042588-A-G

Variant summary

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

The XR_001744323.2(LOC105377979):​n.900-10420A>G 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 0.174 in 152,084 control chromosomes in the GnomAD database, including 5,002 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 0.17 (5002 hom., cov: 32)
• Consequence: LOC105377979 XR_001744323.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831

Genes affected

LOC105377979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377979	XR_001744323.2	n.900-10420A>G		intron_variant, non_coding_transcript_variant
LOC105377979	XR_001744324.2	n.900-10420A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26444 AN: 151966 Hom.: 4991 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.174 AC: 26499 AN: 152084 Hom.: 5002 Cov.: 32 AF XY: 0.169 AC XY: 12563 AN XY: 74340

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.0885

Gnomad4 ASJ AF: 0.0939

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0430

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0591

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0823 Hom.: 1385

Bravo AF: 0.191

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1357056; hg19: chr6-122363734;