rs4991400

Positions:

• chr6-73210712-T-A

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 0.453 in 151,946 control chromosomes in the GnomAD database, including 15,905 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 0.45 (15905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

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: 0.453 AC: 68848 AN: 151828 Hom.: 15900 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.453 AC: 68893 AN: 151946 Hom.: 15905 Cov.: 31 AF XY: 0.447 AC XY: 33210 AN XY: 74260

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.482

Alfa AF: 0.453 Hom.: 1976

Bravo AF: 0.460

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4991400; hg19: chr6-73920435;