chr5-61865583-A-G

Variant names:

• chr5-61865583-A-G
• rs1105682

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 0.464 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.790 AC: 32804 AN: 41542

American (AMR) AF: 0.381 AC: 5812 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2028 AN: 5170

South Asian (SAS) AF: 0.391 AC: 1886 AN: 4818

European-Finnish (FIN) AF: 0.352 AC: 3726 AN: 10586

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21585 AN: 67970

Other (OTH) AF: 0.429 AC: 905 AN: 2108

Alfa AF: 0.274 Hom.: 807

Bravo AF: 0.480

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.18

Splicing

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

Other links and lift over

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