5-61865583-A-G

Variant names:

• chr5-61865583-A-G
• rs1105682

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.464 in 152,136 control chromosomes in the GnomAD database, including 19,634 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 0.46 (19634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.463 AC: 70446 AN: 152018 Hom.: 19590 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.464 AC: 70544 AN: 152136 Hom.: 19634 Cov.: 32 AF XY: 0.462 AC XY: 34362 AN XY: 74376

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.429

Alfa AF: 0.240 Hom.: 569

Bravo AF: 0.480

Asia WGS AF: 0.451 AC: 1567 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	11
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1105682; hg19: chr5-61161410; COSMIC: COSV60141173;