17-37666305-T-C

Variant names:

• chr17-37666305-T-C
• rs6607284
• ENST00000613901.1:n.109-9519T>C

Variant summary

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

The ENST00000615265.1(ENSG00000277688):​n.591-17910T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,088 control chromosomes in the GnomAD database, including 11,791 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 0.39 (11791 hom., cov: 33)
• Consequence: ENSG00000277688 ENST00000615265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 13 publications found

Genes affected

ENSG00000277688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615265.1. 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
	ENSG00000277688	ENST00000613901.1	TSL:4	n.109-9519T>C		intron	N/A
	ENSG00000277688	ENST00000615265.1	TSL:3	n.591-17910T>C		intron	N/A
	ENSG00000277688	ENST00000717157.1		n.430+765T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58987 AN: 151970 Hom.: 11769 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.388 AC: 59064 AN: 152088 Hom.: 11791 Cov.: 33 AF XY: 0.387 AC XY: 28749 AN XY: 74344

African (AFR) AF: 0.385 AC: 15950 AN: 41462

American (AMR) AF: 0.520 AC: 7949 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1739 AN: 5170

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4818

European-Finnish (FIN) AF: 0.338 AC: 3576 AN: 10570

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25807 AN: 68006

Other (OTH) AF: 0.384 AC: 811 AN: 2112

Alfa AF: 0.379 Hom.: 26408

Bravo AF: 0.407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
PhyloP100		-0.18

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: rs6607284;

hg19: chr17-36026335;