chr2-71058744-A-C

Variant names:

• chr2-71058744-A-C
• rs10167593
• ENST00000434990.1:n.61+5939T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434990.1(ENSG00000236469):​n.61+5939T>G variant causes a intron 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: ENSG00000236469 ENST00000434990.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753
• Publications: 6 publications found

Genes affected

ENSG00000236469 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434990.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236469	ENST00000434990.1	TSL:4	n.61+5939T>G		intron	N/A
	ENSG00000236469	ENST00000760092.1		n.61+5939T>G		intron	N/A
	ENSG00000236469	ENST00000760093.1		n.64+5939T>G		intron	N/A

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

African (AFR) AF: 0.133 AC: 5506 AN: 41510

American (AMR) AF: 0.170 AC: 2603 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3470

East Asian (EAS) AF: 0.119 AC: 612 AN: 5160

South Asian (SAS) AF: 0.148 AC: 713 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3311 AN: 10564

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15821 AN: 67994

Other (OTH) AF: 0.194 AC: 408 AN: 2108

Alfa AF: 0.216 Hom.: 5260

Bravo AF: 0.182

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.56
PhyloP100		0.75

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10167593;

hg19: chr2-71285874;