chr4-110728095-C-T

Variant names:

• chr4-110728095-C-T
• rs12647316

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 0.156 in 152,114 control chromosomes in the GnomAD database, including 2,167 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 0.16 (2167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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: 0.156 AC: 23692 AN: 151996 Hom.: 2164 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.156 AC: 23718 AN: 152114 Hom.: 2167 Cov.: 32 AF XY: 0.162 AC XY: 12081 AN XY: 74350

African (AFR) AF: 0.140 AC: 5798 AN: 41492

American (AMR) AF: 0.208 AC: 3181 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1842 AN: 5162

South Asian (SAS) AF: 0.133 AC: 639 AN: 4816

European-Finnish (FIN) AF: 0.150 AC: 1583 AN: 10582

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.133 AC: 9074 AN: 67996

Other (OTH) AF: 0.173 AC: 364 AN: 2106

Alfa AF: 0.164 Hom.: 690

Bravo AF: 0.160

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.19
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs12647316; hg19: chr4-111649251;