rs16975985

Variant names:

• chr17-70637924-A-G
• rs16975985
• ENST00000779441.1:n.160-1951A>G

Variant summary

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

The ENST00000779441.1(ENSG00000301514):​n.160-1951A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,140 control chromosomes in the GnomAD database, including 1,490 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 0.12 (1490 hom., cov: 32)
• Consequence: ENSG00000301514 ENST00000779441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939
• Publications: 5 publications found

Genes affected

ENSG00000301514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 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
ENSG00000301514	ENST00000779441.1	n.160-1951A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18255 AN: 152022 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.120 AC: 18259 AN: 152140 Hom.: 1490 Cov.: 32 AF XY: 0.120 AC XY: 8927 AN XY: 74378

African (AFR) AF: 0.231 AC: 9578 AN: 41486

American (AMR) AF: 0.0875 AC: 1337 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.111 AC: 576 AN: 5176

South Asian (SAS) AF: 0.0706 AC: 341 AN: 4830

European-Finnish (FIN) AF: 0.123 AC: 1302 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0675 AC: 4593 AN: 68002

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.0836 Hom.: 1705

Bravo AF: 0.123

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs16975985; hg19: chr17-68634065;