chr6-73210712-T-A

Variant names:

• chr6-73210712-T-A
• rs4991400
• ENST00000423730.3:n.*350-632A>T

Variant summary

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

The ENST00000423730.3(ENSG00000243501):​n.*350-632A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000243501 ENST00000423730.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

Genes affected

ENSG00000243501 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243501	ENST00000423730.3	n.*350-632A>T		intron_variant	Intron 7 of 7	5		ENSP00000457270.2

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;