rs1535842

Positions:

• chr9-2212546-G-A
• chr9-2212546-G-C

Variant summary

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

The XR_007061395.1(LOC107987043):​n.301+18035C>T 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 0.578 in 152,020 control chromosomes in the GnomAD database, including 26,970 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 (26970 hom., cov: 32)
• Consequence: LOC107987043 XR_007061395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

Genes affected

LOC107987043 (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 (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987043	XR_007061395.1	n.301+18035C>T		intron_variant, non_coding_transcript_variant
LOC107987043	XR_001746600.2	n.297+18035C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87826 AN: 151902 Hom.: 26947 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.578 AC: 87890 AN: 152020 Hom.: 26970 Cov.: 32 AF XY: 0.572 AC XY: 42519 AN XY: 74302

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.563

Alfa AF: 0.512 Hom.: 23383

Bravo AF: 0.593

Asia WGS AF: 0.488 AC: 1700 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535842; hg19: chr9-2212546;