4-171230560-C-G

Variant names:

• chr4-171230560-C-G
• rs958355

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.888 in 152,228 control chromosomes in the GnomAD database, including 60,126 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 0.89 (60126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.03
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.888 AC: 135096 AN: 152110 Hom.: 60078 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.888 AC: 135200 AN: 152228 Hom.: 60126 Cov.: 32 AF XY: 0.892 AC XY: 66396 AN XY: 74428

African (AFR) AF: 0.862 AC: 35782 AN: 41502

American (AMR) AF: 0.924 AC: 14136 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3072 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4829 AN: 5178

South Asian (SAS) AF: 0.924 AC: 4458 AN: 4826

European-Finnish (FIN) AF: 0.926 AC: 9832 AN: 10614

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60146 AN: 68010

Other (OTH) AF: 0.892 AC: 1888 AN: 2116

Alfa AF: 0.877 Hom.: 2845

Bravo AF: 0.886

Asia WGS AF: 0.910 AC: 3162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.35
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs958355; hg19: chr4-172151711;