rs1644305

Variant names:

• chr5-133867905-G-A
• rs1644305

Your query was ambiguous. Multiple possible variants found:

• chr5-133867905-G-A
• chr5-133867905-G-C
• chr5-133867905-G-T

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 0.359 in 151,980 control chromosomes in the GnomAD database, including 10,171 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 (10171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 10 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 (NFE) allele frequency at 95% confidence interval = 0.419 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: 0.359 AC: 54552 AN: 151862 Hom.: 10165 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.359 AC: 54584 AN: 151980 Hom.: 10171 Cov.: 31 AF XY: 0.349 AC XY: 25958 AN XY: 74314

African (AFR) AF: 0.316 AC: 13096 AN: 41404

American (AMR) AF: 0.301 AC: 4592 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3470

East Asian (EAS) AF: 0.150 AC: 779 AN: 5182

South Asian (SAS) AF: 0.296 AC: 1424 AN: 4812

European-Finnish (FIN) AF: 0.299 AC: 3155 AN: 10566

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28723 AN: 67956

Other (OTH) AF: 0.366 AC: 772 AN: 2108

Alfa AF: 0.361 Hom.: 4129

Bravo AF: 0.352

Asia WGS AF: 0.227 AC: 791 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	1.3
DANN	Benign	0.66
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs1644305; hg19: chr5-133203596;