14-53947414-A-G

Variant names:

• chr14-53947414-A-G
• rs11623717

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 0.36 in 151,362 control chromosomes in the GnomAD database, including 10,286 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 (10286 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.360 AC: 54431 AN: 151258 Hom.: 10290 Cov.: 29

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.360 AC: 54442 AN: 151362 Hom.: 10286 Cov.: 29 AF XY: 0.362 AC XY: 26778 AN XY: 73894

African (AFR) AF: 0.234 AC: 9673 AN: 41304

American (AMR) AF: 0.425 AC: 6457 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1594 AN: 3462

East Asian (EAS) AF: 0.425 AC: 2176 AN: 5124

South Asian (SAS) AF: 0.477 AC: 2268 AN: 4750

European-Finnish (FIN) AF: 0.344 AC: 3559 AN: 10348

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27366 AN: 67866

Other (OTH) AF: 0.390 AC: 820 AN: 2100

Alfa AF: 0.379 Hom.: 9060

Bravo AF: 0.358

Asia WGS AF: 0.450 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.38
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11623717; hg19: chr14-54414132;