4-183360114-C-T

Variant names:

• chr4-183360114-C-T
• rs1113122

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 0.582 in 151,462 control chromosomes in the GnomAD database, including 26,039 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 0.58 (26039 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 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: 0.582 AC: 88061 AN: 151344 Hom.: 26027 Cov.: 28

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.667

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.582 AC: 88108 AN: 151462 Hom.: 26039 Cov.: 28 AF XY: 0.586 AC XY: 43380 AN XY: 73984

African (AFR) AF: 0.546 AC: 22515 AN: 41214

American (AMR) AF: 0.689 AC: 10476 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2264 AN: 3464

East Asian (EAS) AF: 0.796 AC: 4077 AN: 5122

South Asian (SAS) AF: 0.586 AC: 2795 AN: 4770

European-Finnish (FIN) AF: 0.613 AC: 6440 AN: 10504

Middle Eastern (MID) AF: 0.669 AC: 194 AN: 290

European-Non Finnish (NFE) AF: 0.555 AC: 37676 AN: 67892

Other (OTH) AF: 0.588 AC: 1233 AN: 2098

Alfa AF: 0.575 Hom.: 9637

Bravo AF: 0.591

Asia WGS AF: 0.662 AC: 2300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1113122; hg19: chr4-184281267;