4-11605877-G-C

Variant names:

• chr4-11605877-G-C
• rs10488990
• NR_188483.1:n.267+53923G>C

Variant summary

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

The NR_188483.1(LOC107986178):​n.267+53923G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,030 control chromosomes in the GnomAD database, including 799 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 0.10 (799 hom., cov: 32)
• Consequence: LOC107986178 NR_188483.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 1 publications found

Genes affected

LOC107986178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986178	NR_188483.1	n.267+53923G>C		intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15195 AN: 151910 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.100 AC: 15199 AN: 152030 Hom.: 799 Cov.: 32 AF XY: 0.103 AC XY: 7643 AN XY: 74308

African (AFR) AF: 0.0894 AC: 3709 AN: 41470

American (AMR) AF: 0.0673 AC: 1027 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0721 AC: 250 AN: 3468

East Asian (EAS) AF: 0.190 AC: 983 AN: 5164

South Asian (SAS) AF: 0.150 AC: 722 AN: 4810

European-Finnish (FIN) AF: 0.137 AC: 1444 AN: 10566

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6764 AN: 67974

Other (OTH) AF: 0.100 AC: 212 AN: 2110

Alfa AF: 0.0954 Hom.: 87

Bravo AF: 0.0928

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.45
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10488990; hg19: chr4-11607501;