rs4756344

Positions:

• chr11-36743734-G-A

Variant summary

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

The XR_001748187.1(LOC107984326):​n.576+32927G>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 0.705 in 152,084 control chromosomes in the GnomAD database, including 38,354 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 0.70 (38354 hom., cov: 32)
• Consequence: LOC107984326 XR_001748187.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

Genes affected

LOC107984326 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984326	XR_001748187.1	n.576+32927G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107100 AN: 151966 Hom.: 38317 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.705 AC: 107195 AN: 152084 Hom.: 38354 Cov.: 32 AF XY: 0.698 AC XY: 51863 AN XY: 74340

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.710

Alfa AF: 0.731 Hom.: 23491

Bravo AF: 0.699

Asia WGS AF: 0.479 AC: 1666 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	0.89
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4756344; hg19: chr11-36765284;