rs723149

Positions:

• chr7-46537458-A-G
• chr7-46537458-A-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 0.65 in 152,200 control chromosomes in the GnomAD database, including 34,126 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 0.65 (34126 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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: 0.650 AC: 98800 AN: 152084 Hom.: 34064 Cov.: 33

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.650 AC: 98917 AN: 152200 Hom.: 34126 Cov.: 33 AF XY: 0.646 AC XY: 48054 AN XY: 74402

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.624

Alfa AF: 0.568 Hom.: 33504

Bravo AF: 0.653

Asia WGS AF: 0.733 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723149; hg19: chr7-46577056;