rs9891949

Positions:

• chr17-8195865-G-A

Variant summary

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

The XR_007065604.1(LOC124903913):​n.1016+3348C>T 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 0.637 in 151,970 control chromosomes in the GnomAD database, including 31,196 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 0.64 (31196 hom., cov: 33)
• Consequence: LOC124903913 XR_007065604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LOC124903913 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903913	XR_007065604.1	n.1016+3348C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96793 AN: 151850 Hom.: 31175 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.637 AC: 96862 AN: 151970 Hom.: 31196 Cov.: 33 AF XY: 0.644 AC XY: 47843 AN XY: 74300

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.634

Alfa AF: 0.657 Hom.: 5591

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.89
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9891949; hg19: chr17-8099183;