rs16970398

Variant names:

• chr17-34804715-G-A
• rs16970398
• XR_001752847.2:n.3743C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-34804715-G-A
• chr17-34804715-G-C
• chr17-34804715-G-T

Variant summary

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

The XR_001752847.2(LOC105371742):​n.3743C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 140,938 control chromosomes in the GnomAD database, including 989 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 0.10 (989 hom., cov: 26)
• Consequence: LOC105371742 XR_001752847.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 1 publications found

Genes affected

LOC105371742 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.105 AC: 14748 AN: 140848 Hom.: 983 Cov.: 26

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.105 AC: 14763 AN: 140938 Hom.: 989 Cov.: 26 AF XY: 0.106 AC XY: 7149 AN XY: 67338

African (AFR) AF: 0.0606 AC: 2278 AN: 37598

American (AMR) AF: 0.126 AC: 1598 AN: 12724

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 486 AN: 3430

East Asian (EAS) AF: 0.281 AC: 1337 AN: 4760

South Asian (SAS) AF: 0.220 AC: 948 AN: 4312

European-Finnish (FIN) AF: 0.0432 AC: 357 AN: 8260

Middle Eastern (MID) AF: 0.237 AC: 62 AN: 262

European-Non Finnish (NFE) AF: 0.111 AC: 7388 AN: 66754

Other (OTH) AF: 0.122 AC: 237 AN: 1938

Alfa AF: 0.0577 Hom.: 75

Bravo AF: 0.106

Asia WGS AF: 0.206 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0060
DANN	Benign	0.73
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs16970398; hg19: chr17-33131734;