17-37665106-T-C

Variant names:

• chr17-37665106-T-C
• rs12449449
• ENST00000613901.1:n.109-10718T>C

Variant summary

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

The ENST00000615265.1(ENSG00000277688):​n.591-19109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,212 control chromosomes in the GnomAD database, including 4,203 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 0.21 (4203 hom., cov: 32)
• Consequence: ENSG00000277688 ENST00000615265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 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=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 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.109-10718T>C		intron	N/A
	ENSG00000277688	ENST00000615265.1	TSL:3	n.591-19109T>C		intron	N/A
	ENSG00000277688	ENST00000717157.1		n.266-270T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32356 AN: 152094 Hom.: 4185 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.213 AC: 32396 AN: 152212 Hom.: 4203 Cov.: 32 AF XY: 0.213 AC XY: 15872 AN XY: 74416

African (AFR) AF: 0.101 AC: 4190 AN: 41560

American (AMR) AF: 0.408 AC: 6232 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 751 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1500 AN: 5170

South Asian (SAS) AF: 0.194 AC: 935 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1690 AN: 10594

Middle Eastern (MID) AF: 0.310 AC: 90 AN: 290

European-Non Finnish (NFE) AF: 0.241 AC: 16404 AN: 67990

Other (OTH) AF: 0.233 AC: 494 AN: 2116

Alfa AF: 0.234 Hom.: 555

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		0.16

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: rs12449449;

hg19: chr17-36025136;