rs4618379

Positions:

• chr4-69049206-T-C

Variant summary

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

The XR_001741714.2(LOC105377265):​n.3242-445A>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 0.201 in 152,014 control chromosomes in the GnomAD database, including 3,232 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 0.20 (3232 hom., cov: 32)
• Consequence: LOC105377265 XR_001741714.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688

Genes affected

LOC105377265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377265	XR_001741714.2	n.3242-445A>G		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938851.2	n.510-445A>G		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938852.2	n.402-445A>G		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938854.2	n.492-445A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30571 AN: 151896 Hom.: 3231 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.201 AC: 30588 AN: 152014 Hom.: 3232 Cov.: 32 AF XY: 0.201 AC XY: 14905 AN XY: 74312

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.197

Alfa AF: 0.181 Hom.: 339

Bravo AF: 0.198

Asia WGS AF: 0.190 AC: 656 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4618379; hg19: chr4-69914924;