XM_047427955.1:c.*103G>A

Variant names:

• chr11-1056981-G-A
• rs7112267
• XM_047427955.1:c.*103G>A

Variant summary

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

The XM_047427955.1(LOC124902605):​c.*103G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,138 control chromosomes in the GnomAD database, including 818 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 0.090 (818 hom., cov: 33)
• Consequence: LOC124902605 XM_047427955.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 1 publications found

Genes affected

LOC124902605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902605	XM_047427955.1	c.*103G>A		3_prime_UTR_variant	Exon 4 of 4		XP_047283911.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 13646 AN: 152020 Hom.: 819 Cov.: 33

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0897 AC: 13642 AN: 152138 Hom.: 818 Cov.: 33 AF XY: 0.0924 AC XY: 6869 AN XY: 74368

African (AFR) AF: 0.0276 AC: 1145 AN: 41508

American (AMR) AF: 0.0486 AC: 744 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1344 AN: 5188

South Asian (SAS) AF: 0.125 AC: 603 AN: 4820

European-Finnish (FIN) AF: 0.163 AC: 1723 AN: 10564

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7645 AN: 67976

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.105 Hom.: 333

Bravo AF: 0.0765

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.22
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7112267; hg19: chr11-1056981;