chr4-48976224-T-G

Variant names:

• chr4-48976224-T-G
• rs2572357

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 0.582 in 151,944 control chromosomes in the GnomAD database, including 29,190 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 0.58 (29190 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 5 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 (AMR) allele frequency at 95% confidence interval = 0.735 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: 0.582 AC: 88350 AN: 151826 Hom.: 29181 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.582 AC: 88383 AN: 151944 Hom.: 29190 Cov.: 31 AF XY: 0.583 AC XY: 43327 AN XY: 74262

African (AFR) AF: 0.266 AC: 11036 AN: 41412

American (AMR) AF: 0.746 AC: 11398 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2728 AN: 3466

East Asian (EAS) AF: 0.294 AC: 1517 AN: 5160

South Asian (SAS) AF: 0.533 AC: 2564 AN: 4812

European-Finnish (FIN) AF: 0.742 AC: 7831 AN: 10548

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.722 AC: 49072 AN: 67956

Other (OTH) AF: 0.634 AC: 1339 AN: 2112

Alfa AF: 0.528 Hom.: 6491

Bravo AF: 0.572

Asia WGS AF: 0.445 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.41
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2572357; hg19: chr4-48978241;