rs370672

Variant names:

• chr5-2448032-G-A
• rs370672

Your query was ambiguous. Multiple possible variants found:

• chr5-2448032-G-A
• chr5-2448032-G-C
• chr5-2448032-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 0.341 in 152,064 control chromosomes in the GnomAD database, including 9,770 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 0.34 (9770 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.341 AC: 51797 AN: 151946 Hom.: 9769 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.341 AC: 51836 AN: 152064 Hom.: 9770 Cov.: 33 AF XY: 0.353 AC XY: 26206 AN XY: 74328

African (AFR) AF: 0.299 AC: 12413 AN: 41490

American (AMR) AF: 0.394 AC: 6011 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 703 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4421 AN: 5164

South Asian (SAS) AF: 0.569 AC: 2745 AN: 4824

European-Finnish (FIN) AF: 0.375 AC: 3955 AN: 10556

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20554 AN: 67964

Other (OTH) AF: 0.328 AC: 694 AN: 2114

Alfa AF: 0.296 Hom.: 7941

Bravo AF: 0.337

Asia WGS AF: 0.673 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
DANN	Benign	0.37
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs370672; hg19: chr5-2448146;