4-181310165-A-G

Position:

• chr4-181310165-A-G

Variant summary

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

The variant allele was found at a frequency of 0.0752 in 152,210 control chromosomes in the GnomAD database, including 601 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 0.075 (601 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11430 AN: 152092 Hom.: 599 Cov.: 31

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0752 AC: 11443 AN: 152210 Hom.: 601 Cov.: 31 AF XY: 0.0794 AC XY: 5906 AN XY: 74406

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0801

Gnomad4 OTH AF: 0.0782

Alfa AF: 0.0662 Hom.: 244

Bravo AF: 0.0737

Asia WGS AF: 0.114 AC: 394 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520474; hg19: chr4-182231318;