rs660727

Variant names:

• chr11-102860343-A-G
• rs660727
• XR_007062868.1:n.1991+4560A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-102860343-A-G
• chr11-102860343-A-T

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+4560A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
LOC124902741	XR_007062868.1	n.1991+4560A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.188 AC: 7814 AN: 41458

American (AMR) AF: 0.0693 AC: 1059 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3472

East Asian (EAS) AF: 0.109 AC: 565 AN: 5174

South Asian (SAS) AF: 0.0936 AC: 451 AN: 4820

European-Finnish (FIN) AF: 0.0407 AC: 432 AN: 10604

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

European-Non Finnish (NFE) AF: 0.0527 AC: 3583 AN: 67974

Other (OTH) AF: 0.102 AC: 214 AN: 2106

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs660727; hg19: chr11-102731074;