chr11-1057948-G-C

Variant names:

• chr11-1057948-G-C
• rs12574439
• XM_047427955.1:c.*1070G>C

Variant summary

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

The XM_047427955.1(LOC124902605):​c.*1070G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,258 control chromosomes in the GnomAD database, including 1,763 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 0.14 (1763 hom., cov: 32)
• Consequence: LOC124902605 XM_047427955.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902605	XM_047427955.1	c.*1070G>C		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: 0.141 AC: 21500 AN: 152140 Hom.: 1760 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.141 AC: 21515 AN: 152258 Hom.: 1763 Cov.: 32 AF XY: 0.142 AC XY: 10575 AN XY: 74452

African (AFR) AF: 0.153 AC: 6374 AN: 41528

American (AMR) AF: 0.0964 AC: 1475 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 845 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1323 AN: 5186

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4822

European-Finnish (FIN) AF: 0.0778 AC: 826 AN: 10612

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8537 AN: 68010

Other (OTH) AF: 0.146 AC: 308 AN: 2116

Alfa AF: 0.124 Hom.: 164

Bravo AF: 0.143

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.45
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs12574439; hg19: chr11-1057948;