4-124417451-G-C

Position:

• chr4-124417451-G-C

Variant summary

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

The XR_001741822.2(LOC105377408):​n.77+2811C>G 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 0.306 in 151,882 control chromosomes in the GnomAD database, including 7,407 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 0.31 (7407 hom., cov: 32)
• Consequence: LOC105377408 XR_001741822.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

Genes affected

LOC105377408 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377408	XR_001741822.2	n.77+2811C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46452 AN: 151764 Hom.: 7406 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.306 AC: 46491 AN: 151882 Hom.: 7407 Cov.: 32 AF XY: 0.307 AC XY: 22760 AN XY: 74186

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.341

Alfa AF: 0.204 Hom.: 450

Bravo AF: 0.301

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518433; hg19: chr4-125338606;