4-64789270-A-G

Position:

• chr4-64789270-A-G

Variant summary

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

The XR_001741712.2(LOC107986284):​n.383+13226A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.218 in 152,004 control chromosomes in the GnomAD database, including 4,082 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 0.22 (4082 hom., cov: 32)
• Consequence: LOC107986284 XR_001741712.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.02

Genes affected

LOC107986284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986284	XR_001741712.2	n.383+13226A>G		intron_variant, non_coding_transcript_variant
LOC107986284	XR_001741711.2	n.204+14445A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33141 AN: 151886 Hom.: 4088 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.218 AC: 33138 AN: 152004 Hom.: 4082 Cov.: 32 AF XY: 0.223 AC XY: 16537 AN XY: 74296

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.259

Alfa AF: 0.224 Hom.: 5024

Bravo AF: 0.222

Asia WGS AF: 0.369 AC: 1285 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11731709; hg19: chr4-65654988;