13-70891971-C-T

Variant names:

• chr13-70891971-C-T
• rs1937070
• ENST00000816890.1:n.113-4958C>T

Variant summary

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

The ENST00000816890.1(ENSG00000306305):​n.113-4958C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,110 control chromosomes in the GnomAD database, including 6,129 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 0.27 (6129 hom., cov: 31)
• Consequence: ENSG00000306305 ENST00000816890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 1 publications found

Genes affected

ENSG00000306305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816890.1. 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
	ENSG00000306305	ENST00000816890.1		n.113-4958C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40191 AN: 150992 Hom.: 6119 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.266 AC: 40216 AN: 151110 Hom.: 6129 Cov.: 31 AF XY: 0.274 AC XY: 20226 AN XY: 73804

African (AFR) AF: 0.128 AC: 5303 AN: 41350

American (AMR) AF: 0.371 AC: 5614 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1212 AN: 3460

East Asian (EAS) AF: 0.379 AC: 1950 AN: 5150

South Asian (SAS) AF: 0.313 AC: 1505 AN: 4806

European-Finnish (FIN) AF: 0.416 AC: 4355 AN: 10472

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.289 AC: 19512 AN: 67446

Other (OTH) AF: 0.268 AC: 561 AN: 2092

Alfa AF: 0.219 Hom.: 744

Bravo AF: 0.259

Asia WGS AF: 0.278 AC: 958 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.17
DANN	Benign	0.23
PhyloP100		-0.31

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: rs1937070;

hg19: chr13-71466103;