XM_047427980.1:c.*1058-7737G>T

Variant names:

• chr11-65811201-C-A
• rs11227306
• XM_047427980.1:c.*1058-7737G>T

Variant summary

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

The XM_047427980.1(LOC124902693):​c.*1058-7737G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,828 control chromosomes in the GnomAD database, including 7,924 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 0.31 (7924 hom., cov: 32)
• Consequence: LOC124902693 XM_047427980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 21 publications found

Genes affected

LOC124902693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902693	XM_047427980.1	c.*1058-7737G>T		intron_variant	Intron 3 of 6		XP_047283936.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47680 AN: 151710 Hom.: 7907 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.314 AC: 47730 AN: 151828 Hom.: 7924 Cov.: 32 AF XY: 0.305 AC XY: 22661 AN XY: 74234

African (AFR) AF: 0.267 AC: 11015 AN: 41254

American (AMR) AF: 0.281 AC: 4296 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1550 AN: 5164

South Asian (SAS) AF: 0.131 AC: 632 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2905 AN: 10586

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25094 AN: 67962

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.349 Hom.: 20828

Bravo AF: 0.317

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs11227306; hg19: chr11-65578672;