chr14-48095753-G-A

Variant names:

• chr14-48095753-G-A
• rs7151223

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 0.335 in 151,976 control chromosomes in the GnomAD database, including 9,049 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 0.34 (9049 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 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: 0.336 AC: 50961 AN: 151858 Hom.: 9048 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.335 AC: 50981 AN: 151976 Hom.: 9049 Cov.: 33 AF XY: 0.330 AC XY: 24487 AN XY: 74278

African (AFR) AF: 0.387 AC: 16038 AN: 41432

American (AMR) AF: 0.282 AC: 4297 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3468

East Asian (EAS) AF: 0.0536 AC: 277 AN: 5166

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4820

European-Finnish (FIN) AF: 0.264 AC: 2783 AN: 10552

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23622 AN: 67972

Other (OTH) AF: 0.342 AC: 724 AN: 2114

Alfa AF: 0.339 Hom.: 41406

Bravo AF: 0.336

Asia WGS AF: 0.189 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.62
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs7151223; hg19: chr14-48564956;