4-170109656-T-C

Variant names:

• chr4-170109656-T-C
• rs17628931

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;