chr11-102855974-G-A

Variant names:

• chr11-102855974-G-A
• rs615932
• XR_007062868.1:n.1991+191G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062868.1(LOC124902741):​n.1991+191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0968 in 152,124 control chromosomes in the GnomAD database, including 979 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 (979 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 5 publications found

Genes affected

LOC124902741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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 rank	MANE	Protein	UniProt
LOC124902741	XR_007062868.1	n.1991+191G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14723 AN: 152006 Hom.: 975 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0968 AC: 14729 AN: 152124 Hom.: 979 Cov.: 32 AF XY: 0.0953 AC XY: 7089 AN XY: 74354

African (AFR) AF: 0.188 AC: 7800 AN: 41468

American (AMR) AF: 0.0693 AC: 1060 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3468

East Asian (EAS) AF: 0.110 AC: 570 AN: 5178

South Asian (SAS) AF: 0.0983 AC: 473 AN: 4812

European-Finnish (FIN) AF: 0.0409 AC: 433 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3587 AN: 68012

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.0818 Hom.: 119

Bravo AF: 0.103

Asia WGS AF: 0.112 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.79
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs615932; hg19: chr11-102726705; COSMIC: COSV70064524;