chr7-153181248-A-G

Variant names:

• chr7-153181248-A-G
• rs4285401

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 0.413 in 151,972 control chromosomes in the GnomAD database, including 15,296 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 0.41 (15296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.413 AC: 62782 AN: 151854 Hom.: 15298 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.413 AC: 62771 AN: 151972 Hom.: 15296 Cov.: 32 AF XY: 0.407 AC XY: 30240 AN XY: 74276

Gnomad4 AFR AF: 0.156 AC: 0.156141 AN: 0.156141

Gnomad4 AMR AF: 0.400 AC: 0.400105 AN: 0.400105

Gnomad4 ASJ AF: 0.554 AC: 0.553664 AN: 0.553664

Gnomad4 EAS AF: 0.236 AC: 0.235864 AN: 0.235864

Gnomad4 SAS AF: 0.466 AC: 0.465711 AN: 0.465711

Gnomad4 FIN AF: 0.497 AC: 0.497443 AN: 0.497443

Gnomad4 NFE AF: 0.560 AC: 0.559823 AN: 0.559823

Gnomad4 OTH AF: 0.418 AC: 0.418009 AN: 0.418009

Alfa AF: 0.507 Hom.: 70783

Bravo AF: 0.390

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4285401; hg19: chr7-152878333;