rs1107680

Variant names:

• chr4-189386130-G-A
• rs1107680
• XR_939634.2:n.301-5415G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The XR_939634.2(LOC105377614):​n.301-5415G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 0 publications found

Genes affected

LOC105377614 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105377614	XR_939634.2	n.301-5415G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.153 AC: 6360 AN: 41498

American (AMR) AF: 0.343 AC: 5233 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3464

East Asian (EAS) AF: 0.432 AC: 2228 AN: 5156

South Asian (SAS) AF: 0.380 AC: 1833 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4260 AN: 10556

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19574 AN: 67998

Other (OTH) AF: 0.257 AC: 543 AN: 2116

Alfa AF: 0.271 Hom.: 7063

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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1107680; hg19: chr4-190307284;