rs10501636

Positions:

• chr11-87401277-T-C
• chr11-87401277-T-G

Variant summary

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

The XR_002957260.2(LOC107984361):​n.395+28409T>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 0.3 in 152,080 control chromosomes in the GnomAD database, including 8,178 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 0.30 (8178 hom., cov: 32)
• Consequence: LOC107984361 XR_002957260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

LOC107984361 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984361	XR_002957260.2	n.395+28409T>C		intron_variant, non_coding_transcript_variant
LOC107984361	XR_001748316.2	n.318+38801T>C		intron_variant, non_coding_transcript_variant
LOC107984361	XR_002957261.2	n.318+38801T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45706 AN: 151962 Hom.: 8185 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.300 AC: 45687 AN: 152080 Hom.: 8178 Cov.: 32 AF XY: 0.295 AC XY: 21919 AN XY: 74324

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.337

Alfa AF: 0.339 Hom.: 1630

Bravo AF: 0.293

Asia WGS AF: 0.177 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501636; hg19: chr11-87112319;