rs10167593

chr2-71058744-A-C

Variant summary

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

The ENST00000434990.1(ENSG00000236469):n.61+5939T>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 0.197 in 152,128 control chromosomes in the GnomAD database, including 3,162 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 (3162 hom., cov: 32)
• Consequence: ENST00000434990.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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
	ENST00000434990.1	n.61+5939T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29920 AN: 152008 Hom.: 3160 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.197 AC: 29949 AN: 152128 Hom.: 3162 Cov.: 32 AF XY: 0.200 AC XY: 14898 AN XY: 74358

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.194

Alfa AF: 0.218 Hom.: 3736

Bravo AF: 0.182

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.0
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10167593; hg19: chr2-71285874;