rs10483889

Variant names:

• chr14-78091162-T-G
• rs10483889

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 0.148 in 152,222 control chromosomes in the GnomAD database, including 2,196 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 0.15 (2196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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: 0.148 AC: 22527 AN: 152104 Hom.: 2197 Cov.: 32

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.148 AC: 22516 AN: 152222 Hom.: 2196 Cov.: 32 AF XY: 0.149 AC XY: 11089 AN XY: 74414

African (AFR) AF: 0.0378 AC: 1570 AN: 41560

American (AMR) AF: 0.121 AC: 1856 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3468

East Asian (EAS) AF: 0.0398 AC: 206 AN: 5180

South Asian (SAS) AF: 0.192 AC: 923 AN: 4818

European-Finnish (FIN) AF: 0.228 AC: 2419 AN: 10600

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14190 AN: 67978

Other (OTH) AF: 0.171 AC: 361 AN: 2116

Alfa AF: 0.186 Hom.: 5426

Bravo AF: 0.132

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs10483889; hg19: chr14-78557505;