rs17142039

Positions:

• chr7-19808525-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745112.2(LOC107986774):​n.1126-2720T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.024 in 152,178 control chromosomes in the GnomAD database, including 182 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 0.024 (182 hom., cov: 32)
• Consequence: LOC107986774 XR_001745112.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

Genes affected

LOC107986774 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986774	XR_001745112.2	n.1126-2720T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0240 AC: 3656 AN: 152060 Hom.: 183 Cov.: 32

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00391

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0240 AC: 3658 AN: 152178 Hom.: 182 Cov.: 32 AF XY: 0.0248 AC XY: 1845 AN XY: 74412

Gnomad4 AFR AF: 0.0443

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00390

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.00927 Hom.: 27

Bravo AF: 0.0268

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17142039; hg19: chr7-19848148;