rs1110386

Variant names:

• chr14-95052503-C-T
• rs1110386

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 0.221 in 152,144 control chromosomes in the GnomAD database, including 3,866 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 0.22 (3866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 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: 0.221 AC: 33533 AN: 152026 Hom.: 3858 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.221 AC: 33567 AN: 152144 Hom.: 3866 Cov.: 32 AF XY: 0.217 AC XY: 16118 AN XY: 74386

African (AFR) AF: 0.201 AC: 8353 AN: 41486

American (AMR) AF: 0.275 AC: 4201 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1092 AN: 5174

South Asian (SAS) AF: 0.297 AC: 1429 AN: 4812

European-Finnish (FIN) AF: 0.115 AC: 1222 AN: 10618

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15687 AN: 67982

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.237 Hom.: 7391

Bravo AF: 0.229

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.64
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1110386; hg19: chr14-95518840;