chr4-180410693-A-T

Variant names:

• chr4-180410693-A-T
• rs2309248
• XR_001741469.2:n.1399+10208A>T

Variant summary

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

The XR_001741469.2(LOC105377567):​n.1399+10208A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,900 control chromosomes in the GnomAD database, including 24,823 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 0.56 (24823 hom., cov: 32)
• Consequence: LOC105377567 XR_001741469.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

Genes affected

LOC105377567 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377567	XR_001741469.2	n.1399+10208A>T		intron_variant	Intron 2 of 3
LOC105377567	XR_007058394.1	n.2209+10208A>T		intron_variant	Intron 1 of 2
LOC105377567	XR_007058395.1	n.1310+10208A>T		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85261 AN: 151782 Hom.: 24817 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.562 AC: 85315 AN: 151900 Hom.: 24823 Cov.: 32 AF XY: 0.554 AC XY: 41090 AN XY: 74206

African (AFR) AF: 0.412 AC: 17067 AN: 41450

American (AMR) AF: 0.582 AC: 8878 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3468

East Asian (EAS) AF: 0.656 AC: 3373 AN: 5138

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4820

European-Finnish (FIN) AF: 0.512 AC: 5403 AN: 10546

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43518 AN: 67908

Other (OTH) AF: 0.604 AC: 1274 AN: 2108

Alfa AF: 0.505 Hom.: 1588

Bravo AF: 0.561

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2309248; hg19: chr4-181331846;