rs1107680

Positions:

• chr4-189386130-G-A
• chr4-189386130-G-C

Variant summary

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

The XR_939634.2(LOC105377614):​n.301-5415G>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 0.271 in 152,082 control chromosomes in the GnomAD database, including 6,217 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 0.27 (6217 hom., cov: 33)
• Consequence: LOC105377614 XR_939634.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731

Genes affected

LOC105377614 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377614	XR_939634.2	n.301-5415G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41140 AN: 151964 Hom.: 6213 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.271 AC: 41157 AN: 152082 Hom.: 6217 Cov.: 33 AF XY: 0.278 AC XY: 20702 AN XY: 74342

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.257

Alfa AF: 0.273 Hom.: 5265

Bravo AF: 0.259

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1107680; hg19: chr4-190307284;