rs1562902

Positions:

• chr11-14896670-C-T

Variant summary

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

The XR_007062603.1(LOC124902638):​n.1485-2275C>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 0.556 in 151,944 control chromosomes in the GnomAD database, including 23,738 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 0.56 (23738 hom., cov: 31)
• Consequence: LOC124902638 XR_007062603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

LOC124902638 (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 (AMR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902638	XR_007062603.1	n.1485-2275C>T		intron_variant, non_coding_transcript_variant
LOC124902638	XR_007062604.1	n.1485-2286C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84344 AN: 151826 Hom.: 23714 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.556 AC: 84425 AN: 151944 Hom.: 23738 Cov.: 31 AF XY: 0.560 AC XY: 41615 AN XY: 74248

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.540

Alfa AF: 0.565 Hom.: 42065

Bravo AF: 0.556

Asia WGS AF: 0.552 AC: 1920 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	0.20
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562902; hg19: chr11-14918216;