rs4067228

Positions:

• chr7-130719948-G-A
• chr7-130719948-G-C
• chr7-130719948-G-T

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 0.56 in 151,904 control chromosomes in the GnomAD database, including 23,996 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 0.56 (23996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84995 AN: 151786 Hom.: 23978 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.560 AC: 85051 AN: 151904 Hom.: 23996 Cov.: 31 AF XY: 0.559 AC XY: 41459 AN XY: 74216

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.570

Alfa AF: 0.549 Hom.: 25940

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4067228; hg19: chr7-130404776;