4-107553429-G-T

Variant names:

• chr4-107553429-G-T
• rs1514728
• XR_939059.3:n.131-6469C>A

Variant summary

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

The XR_939059.3(LOC105377358):​n.131-6469C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,670 control chromosomes in the GnomAD database, including 30,998 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 0.64 (30998 hom., cov: 33)
• Consequence: LOC105377358 XR_939059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 1 publications found

Genes affected

LOC105377358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377358	XR_939059.3	n.131-6469C>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96701 AN: 151552 Hom.: 30963 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.638 AC: 96782 AN: 151670 Hom.: 30998 Cov.: 33 AF XY: 0.636 AC XY: 47134 AN XY: 74122

African (AFR) AF: 0.667 AC: 27630 AN: 41408

American (AMR) AF: 0.621 AC: 9448 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2194 AN: 3458

East Asian (EAS) AF: 0.517 AC: 2648 AN: 5124

South Asian (SAS) AF: 0.477 AC: 2302 AN: 4822

European-Finnish (FIN) AF: 0.663 AC: 7002 AN: 10558

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43388 AN: 67770

Other (OTH) AF: 0.639 AC: 1350 AN: 2112

Alfa AF: 0.640 Hom.: 114667

Bravo AF: 0.639

Asia WGS AF: 0.484 AC: 1686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.086
DANN	Benign	0.30
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1514728; hg19: chr4-108474586;