rs17544779

Variant names:

• chr17-34793767-A-C
• rs17544779
• XR_001752843.3:n.354-31410T>G

Variant summary

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

The XR_001752843.3(LOC105371742):​n.354-31410T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 152,192 control chromosomes in the GnomAD database, including 790 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 0.087 (790 hom., cov: 32)
• Consequence: LOC105371742 XR_001752843.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371742	XR_001752843.3	n.354-31410T>G		intron_variant	Intron 3 of 3
LOC105371742	XR_001752844.3	n.354-31410T>G		intron_variant	Intron 3 of 4
LOC105371742	XR_001752845.3	n.354-31410T>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13229 AN: 152074 Hom.: 789 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.0869 AC: 13225 AN: 152192 Hom.: 790 Cov.: 32 AF XY: 0.0894 AC XY: 6651 AN XY: 74434

African (AFR) AF: 0.0213 AC: 883 AN: 41550

American (AMR) AF: 0.0890 AC: 1360 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3472

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5184

South Asian (SAS) AF: 0.0670 AC: 323 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1873 AN: 10602

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7953 AN: 67970

Other (OTH) AF: 0.0909 AC: 192 AN: 2112

Alfa AF: 0.105 Hom.: 1132

Bravo AF: 0.0762

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.72
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs17544779; hg19: chr17-33120786;