5-66443611-T-C

Variant names:

• chr5-66443611-T-C
• rs10514995

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 0.399 in 152,082 control chromosomes in the GnomAD database, including 12,425 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 0.40 (12425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60628 AN: 151964 Hom.: 12417 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.399 AC: 60687 AN: 152082 Hom.: 12425 Cov.: 32 AF XY: 0.397 AC XY: 29499 AN XY: 74354

African (AFR) AF: 0.494 AC: 20468 AN: 41464

American (AMR) AF: 0.381 AC: 5830 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 894 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2222 AN: 5166

South Asian (SAS) AF: 0.369 AC: 1783 AN: 4828

European-Finnish (FIN) AF: 0.315 AC: 3322 AN: 10560

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24933 AN: 67984

Other (OTH) AF: 0.387 AC: 817 AN: 2110

Alfa AF: 0.374 Hom.: 38208

Bravo AF: 0.410

Asia WGS AF: 0.354 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.73
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs10514995; hg19: chr5-65739439;