rs8007923

Variant names:

• chr14-104190322-T-C
• rs8007923

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 0.357 in 151,944 control chromosomes in the GnomAD database, including 11,351 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 0.36 (11351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 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: 0.357 AC: 54172 AN: 151826 Hom.: 11337 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.357 AC: 54210 AN: 151944 Hom.: 11351 Cov.: 32 AF XY: 0.357 AC XY: 26532 AN XY: 74226

African (AFR) AF: 0.149 AC: 6192 AN: 41438

American (AMR) AF: 0.413 AC: 6309 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3472

East Asian (EAS) AF: 0.184 AC: 949 AN: 5152

South Asian (SAS) AF: 0.333 AC: 1598 AN: 4804

European-Finnish (FIN) AF: 0.476 AC: 5025 AN: 10552

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31678 AN: 67926

Other (OTH) AF: 0.362 AC: 763 AN: 2108

Alfa AF: 0.418 Hom.: 36792

Bravo AF: 0.337

Asia WGS AF: 0.286 AC: 992 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	3.4
DANN	Benign	0.83
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs8007923; hg19: chr14-104656659;