chr5-547743-A-G

Variant names:

• chr5-547743-A-G
• rs4957070

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.489 in 152,148 control chromosomes in the GnomAD database, including 21,601 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 0.49 (21601 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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: 0.489 AC: 74267 AN: 152028 Hom.: 21557 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.489 AC: 74360 AN: 152148 Hom.: 21601 Cov.: 33 AF XY: 0.481 AC XY: 35784 AN XY: 74376

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.461

Alfa AF: 0.411 Hom.: 1846

Bravo AF: 0.519

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4957070; hg19: chr5-547858; COSMIC: COSV60122519;