rs2190324

Positions:

• chr7-13859821-C-T

Variant summary

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

The ENST00000654062.1(ENSG00000224330):​n.484-798G>A 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 0.198 in 152,082 control chromosomes in the GnomAD database, including 4,198 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 0.20 (4198 hom., cov: 32)
• Consequence: ENST00000654062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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
	ENST00000654062.1	n.484-798G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29964 AN: 151962 Hom.: 4169 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0467

Gnomad SAS AF: 0.0690

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.198 AC: 30052 AN: 152082 Hom.: 4198 Cov.: 32 AF XY: 0.192 AC XY: 14293 AN XY: 74372

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0466

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.0890

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.189

Alfa AF: 0.143 Hom.: 2790

Bravo AF: 0.218

Asia WGS AF: 0.109 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2190324; hg19: chr7-13899446;