rs7591996

chr2-6321289-A-Cchr2-6321289-A-Gchr2-6321289-A-T

Variant summary

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

The ENST00000648803.1(ENSG00000234275):n.52-6343T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,950 control chromosomes in the GnomAD database, including 26,262 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 0.57 (26262 hom., cov: 32)
• Consequence: ENST00000648803.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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
	ENST00000648803.1	n.52-6343T>G		intron_variant, non_coding_transcript_variant
	ENST00000425125.1	n.250+4108T>G		intron_variant, non_coding_transcript_variant		4
	ENST00000650957.2	n.58-6343T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86383 AN: 151832 Hom.: 26200 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.569 AC: 86505 AN: 151950 Hom.: 26262 Cov.: 32 AF XY: 0.573 AC XY: 42542 AN XY: 74286

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.552

Alfa AF: 0.465 Hom.: 23416

Bravo AF: 0.580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7591996; hg19: chr2-6461421;