rs2104362

Positions:

• chr6-33857581-G-A

Variant summary

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

The XR_007059555.1(LOC105375027):​n.237+1143G>A 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 0.69 in 152,022 control chromosomes in the GnomAD database, including 36,559 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 0.69 (36559 hom., cov: 31)
• Consequence: LOC105375027 XR_007059555.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

Genes affected

LOC105375027 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375027	XR_007059555.1	n.237+1143G>A		intron_variant, non_coding_transcript_variant
LOC105375027	XR_007059554.1	n.236+1143G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104869 AN: 151904 Hom.: 36538 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.690 AC: 104935 AN: 152022 Hom.: 36559 Cov.: 31 AF XY: 0.690 AC XY: 51290 AN XY: 74348

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.696

Alfa AF: 0.723 Hom.: 39852

Bravo AF: 0.681

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2104362; hg19: chr6-33825358; COSMIC: COSV66104041;