rs2523477

Variant names:

• chr6-31392612-T-C
• rs2523477
• ENST00000744921.1:n.319T>C

Variant summary

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

The ENST00000744921.1(ENSG00000297040):​n.319T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,824 control chromosomes in the GnomAD database, including 1,207 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 0.10 (1207 hom., cov: 31)
• Consequence: ENSG00000297040 ENST00000744921.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 24 publications found

Genes affected

ENSG00000297040 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744921.1. 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
	ENSG00000297040	ENST00000744921.1		n.319T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297040	ENST00000744920.1		n.120+3171T>C		intron	N/A
	MICA-AS1	ENST00000745027.1		n.567+7442A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15486 AN: 151706 Hom.: 1204 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0722

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00773

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.102 AC: 15502 AN: 151824 Hom.: 1207 Cov.: 31 AF XY: 0.0985 AC XY: 7314 AN XY: 74226

African (AFR) AF: 0.162 AC: 6684 AN: 41278

American (AMR) AF: 0.138 AC: 2093 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0722 AC: 250 AN: 3462

East Asian (EAS) AF: 0.0267 AC: 138 AN: 5164

South Asian (SAS) AF: 0.101 AC: 485 AN: 4818

European-Finnish (FIN) AF: 0.00773 AC: 82 AN: 10606

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5407 AN: 68006

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.0841 Hom.: 1740

Bravo AF: 0.118

Asia WGS AF: 0.0700 AC: 241 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.34
PhyloP100		-0.039

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: rs2523477;

hg19: chr6-31360389;