chr4-102444375-G-T

Variant names:

• chr4-102444375-G-T
• rs13115343
• ENST00000512915.5:n.80+5556C>A

Variant summary

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

The NR_136202.1(LOC105377621):​n.185+5556C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,952 control chromosomes in the GnomAD database, including 11,814 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 0.36 (11814 hom., cov: 32)
• Consequence: LOC105377621 NR_136202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

ENSG00000248161 (HGNC:58149):

LOC105377621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377621	NR_136202.1	n.185+5556C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248161	ENST00000512915.5	n.80+5556C>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55096 AN: 151834 Hom.: 11800 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.363 AC: 55158 AN: 151952 Hom.: 11814 Cov.: 32 AF XY: 0.359 AC XY: 26662 AN XY: 74290

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.0324

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.345

Alfa AF: 0.314 Hom.: 13894

Bravo AF: 0.370

Asia WGS AF: 0.110 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13115343; hg19: chr4-103365532;