rs17161695

Variant names:

• chr7-99367083-T-A
• rs17161695
• ENST00000638617.1:c.983+7345T>A

Variant summary

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

The ENST00000638617.1(ENSG00000284292):​c.983+7345T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,056 control chromosomes in the GnomAD database, including 13,466 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 0.30 (13466 hom., cov: 32)
• Consequence: ENSG00000284292 ENST00000638617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 3 publications found

Genes affected

ENSG00000284292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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
ENSG00000284292	ENST00000638617.1	c.983+7345T>A		intron_variant	Intron 8 of 16	5		ENSP00000491073.1
ENSG00000284292	ENST00000441989.6	n.*1096+3450T>A		intron_variant	Intron 11 of 13	2		ENSP00000412879.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45848 AN: 151938 Hom.: 13408 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.302 AC: 45981 AN: 152056 Hom.: 13466 Cov.: 32 AF XY: 0.299 AC XY: 22249 AN XY: 74306

African (AFR) AF: 0.772 AC: 32016 AN: 41494

American (AMR) AF: 0.209 AC: 3186 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3466

East Asian (EAS) AF: 0.0493 AC: 255 AN: 5170

South Asian (SAS) AF: 0.141 AC: 681 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1726 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6998 AN: 67958

Other (OTH) AF: 0.267 AC: 563 AN: 2112

Alfa AF: 0.223 Hom.: 1021

Bravo AF: 0.326

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.72
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17161695; hg19: chr7-98964706;