rs660727

Positions:

• chr11-102860343-A-G
• chr11-102860343-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.1991+4560A>G 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 0.0967 in 152,098 control chromosomes in the GnomAD database, including 972 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 0.097 (972 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

LOC124902741 (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 = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902741	XR_007062868.1	n.1991+4560A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0967 AC: 14704 AN: 151980 Hom.: 967 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0974

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

GnomAD4 genome AF: 0.0967 AC: 14711 AN: 152098 Hom.: 972 Cov.: 32 AF XY: 0.0951 AC XY: 7074 AN XY: 74366

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0936

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0160 Hom.: 10

Bravo AF: 0.103

Asia WGS AF: 0.109 AC: 378 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	2.8
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs660727; hg19: chr11-102731074;