rs756418

Positions:

• chr4-11546343-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741361.2(LOC107986178):​n.1667-5536C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,250 control chromosomes in the GnomAD database, including 942 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 0.099 (942 hom., cov: 32)
• Consequence: LOC107986178 XR_001741361.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

Genes affected

LOC107986178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986178	XR_001741361.2	n.1667-5536C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15050 AN: 152132 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0989 AC: 15052 AN: 152250 Hom.: 942 Cov.: 32 AF XY: 0.0988 AC XY: 7351 AN XY: 74438

Gnomad4 AFR AF: 0.0292

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0588

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.106

Alfa AF: 0.123 Hom.: 1572

Bravo AF: 0.105

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.67
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs756418; hg19: chr4-11547967;