11-46123950-A-C

Variant names:

• chr11-46123950-A-C
• rs7950474
• XR_931252.4:n.1806A>C

Variant summary

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

The XR_931252.4(LOC105376661):​n.1806A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,074 control chromosomes in the GnomAD database, including 14,253 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 0.42 (14253 hom., cov: 33)
• Consequence: LOC105376661 XR_931252.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 3 publications found

Genes affected

LOC105376661 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376661	XR_931252.4	n.1806A>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255314	ENST00000635144.1	n.203+175A>C		intron_variant	Intron 1 of 3	5
ENSG00000255314	ENST00000649677.1	n.142+778A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64288 AN: 151956 Hom.: 14236 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.423 AC: 64330 AN: 152074 Hom.: 14253 Cov.: 33 AF XY: 0.424 AC XY: 31533 AN XY: 74346

African (AFR) AF: 0.312 AC: 12933 AN: 41476

American (AMR) AF: 0.504 AC: 7715 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1200 AN: 5174

South Asian (SAS) AF: 0.537 AC: 2588 AN: 4820

European-Finnish (FIN) AF: 0.446 AC: 4705 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31605 AN: 67968

Other (OTH) AF: 0.466 AC: 986 AN: 2114

Alfa AF: 0.444 Hom.: 9458

Bravo AF: 0.420

Asia WGS AF: 0.443 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.59
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7950474; hg19: chr11-46145501;