17-37662786-A-G

Variant names:

• chr17-37662786-A-G
• rs4074770
• ENST00000613901.1:n.109-13038A>G

Variant summary

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

The ENST00000613901.1(ENSG00000277688):​n.109-13038A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,122 control chromosomes in the GnomAD database, including 11,483 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 0.35 (11483 hom., cov: 32)
• Consequence: ENSG00000277688 ENST00000613901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000277688	ENST00000613901.1	n.109-13038A>G		intron_variant	Intron 1 of 1	4
ENSG00000277688	ENST00000615265.1	n.590+19250A>G		intron_variant	Intron 1 of 1	3
ENSG00000277688	ENST00000717157.1	n.266-2590A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53678 AN: 152004 Hom.: 11447 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.354 AC: 53784 AN: 152122 Hom.: 11483 Cov.: 32 AF XY: 0.350 AC XY: 26005 AN XY: 74384

African (AFR) AF: 0.581 AC: 24094 AN: 41468

American (AMR) AF: 0.463 AC: 7070 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1448 AN: 5182

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1685 AN: 10602

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16640 AN: 67990

Other (OTH) AF: 0.335 AC: 708 AN: 2114

Alfa AF: 0.279 Hom.: 29842

Bravo AF: 0.391

Asia WGS AF: 0.280 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.78
PhyloP100		-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4074770; hg19: chr17-36022817;