17-71735940-G-T

Variant names:

• chr17-71735940-G-T
• rs2253624
• ENST00000670823.1:n.45+7484C>A

Variant summary

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

The ENST00000670823.1(ENSG00000286387):​n.45+7484C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,078 control chromosomes in the GnomAD database, including 7,054 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 0.19 (7054 hom., cov: 32)
• Consequence: ENSG00000286387 ENST00000670823.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 5 publications found

Genes affected

ENSG00000286387 (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 (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670823.1. 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
	ENSG00000286387	ENST00000670823.1		n.45+7484C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28330 AN: 151960 Hom.: 7019 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.187 AC: 28429 AN: 152078 Hom.: 7054 Cov.: 32 AF XY: 0.186 AC XY: 13802 AN XY: 74334

African (AFR) AF: 0.567 AC: 23472 AN: 41410

American (AMR) AF: 0.0896 AC: 1370 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0397 AC: 138 AN: 3472

East Asian (EAS) AF: 0.137 AC: 711 AN: 5172

South Asian (SAS) AF: 0.105 AC: 508 AN: 4828

European-Finnish (FIN) AF: 0.0544 AC: 576 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0194 AC: 1318 AN: 68010

Other (OTH) AF: 0.146 AC: 309 AN: 2116

Alfa AF: 0.0417 Hom.: 144

Bravo AF: 0.206

Asia WGS AF: 0.164 AC: 571 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	13
DANN	Benign	0.38
PhyloP100		0.13

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: rs2253624;

hg19: chr17-69732081;