rs737693

Positions:

• chr11-102855411-A-T

Variant summary

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

The XR_007062868.1(LOC124902741):​n.1840-221A>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 0.0932 in 152,188 control chromosomes in the GnomAD database, including 943 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 0.093 (943 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

LOC124902741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902741	XR_007062868.1	n.1840-221A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14188 AN: 152070 Hom.: 942 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0932 AC: 14190 AN: 152188 Hom.: 943 Cov.: 32 AF XY: 0.0947 AC XY: 7048 AN XY: 74396

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.0710

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0260

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.115 Hom.: 144

Bravo AF: 0.0798

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs737693; hg19: chr11-102726142;