14-95709641-C-G

Variant names:

• chr14-95709641-C-G
• rs11849538

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 0.196 in 151,864 control chromosomes in the GnomAD database, including 3,576 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 0.20 (3576 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29776 AN: 151746 Hom.: 3576 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.196 AC: 29805 AN: 151864 Hom.: 3576 Cov.: 31 AF XY: 0.200 AC XY: 14872 AN XY: 74200

African (AFR) AF: 0.327 AC: 13517 AN: 41380

American (AMR) AF: 0.170 AC: 2591 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1200 AN: 5142

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4812

European-Finnish (FIN) AF: 0.211 AC: 2221 AN: 10526

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8168 AN: 67964

Other (OTH) AF: 0.160 AC: 336 AN: 2106

Alfa AF: 0.0802 Hom.: 103

Bravo AF: 0.196

Asia WGS AF: 0.235 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.84
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs11849538; hg19: chr14-96175978;