rs7849941

chr9-85130318-A-T

Variant summary

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

The XR_001746809.1(LOC107987088):n.191+12127T>A 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 0.259 in 152,102 control chromosomes in the GnomAD database, including 7,883 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 0.26 (7883 hom., cov: 32)
• Consequence: LOC107987088 XR_001746809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

LOC107987088 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987088	XR_001746809.1	n.191+12127T>A		intron_variant, non_coding_transcript_variant
LOC107987088	XR_001746807.1	n.191+12127T>A		intron_variant, non_coding_transcript_variant
LOC107987088	XR_001746808.1	n.191+12127T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39290 AN: 151984 Hom.: 7853 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.259 AC: 39361 AN: 152102 Hom.: 7883 Cov.: 32 AF XY: 0.255 AC XY: 18957 AN XY: 74370

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0458

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.223

Alfa AF: 0.210 Hom.: 666

Bravo AF: 0.272

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.4
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7849941; hg19: chr9-87745233;