4-170109656-T-C

Position:

• chr4-170109656-T-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 0.0678 in 152,252 control chromosomes in the GnomAD database, including 489 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 0.068 (489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 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: 0.0678 AC: 10322 AN: 152134 Hom.: 489 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0772

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

GnomAD4 genome AF: 0.0678 AC: 10322 AN: 152252 Hom.: 489 Cov.: 32 AF XY: 0.0636 AC XY: 4738 AN XY: 74456

Gnomad4 AFR AF: 0.0203

Gnomad4 AMR AF: 0.0676

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0769

Alfa AF: 0.0840 Hom.: 353

Bravo AF: 0.0673

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17628931; hg19: chr4-171030807;