rs1572075

Positions:

• chr4-44100-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant allele was found at a frequency of 0.00357 in 133,726 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0036 (0 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00358 AC: 478 AN: 133624 Hom.: 0 Cov.: 35

Gnomad AFR AF: 0.00230

Gnomad AMI AF: 0.00253

Gnomad AMR AF: 0.00225

Gnomad ASJ AF: 0.00370

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00612

Gnomad FIN AF: 0.00684

Gnomad MID AF: 0.00746

Gnomad NFE AF: 0.00427

Gnomad OTH AF: 0.00546

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

GnomAD4 genome AF: 0.00357 AC: 478 AN: 133726 Hom.: 0 Cov.: 35 AF XY: 0.00350 AC XY: 228 AN XY: 65208

Gnomad4 AFR AF: 0.00226

Gnomad4 AMR AF: 0.00224

Gnomad4 ASJ AF: 0.00370

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00638

Gnomad4 FIN AF: 0.00684

Gnomad4 NFE AF: 0.00427

Gnomad4 OTH AF: 0.00542

Alfa AF: 0.00666 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1572075; hg19: chr4-44101; COSMIC: COSV74114096;