4-110649067-A-C

Position:

• chr4-110649067-A-C

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 0.283 in 152,080 control chromosomes in the GnomAD database, including 6,354 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 0.28 (6354 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43054 AN: 151962 Hom.: 6347 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.283 AC: 43072 AN: 152080 Hom.: 6354 Cov.: 33 AF XY: 0.284 AC XY: 21101 AN XY: 74354

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.281

Alfa AF: 0.254 Hom.: 7651

Bravo AF: 0.281

Asia WGS AF: 0.223 AC: 775 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448818; hg19: chr4-111570223;