rs7239116

Positions:

• chr18-21906764-T-C
• chr18-21906764-T-G

Variant summary

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

The XR_935276.3(LOC105372016):​n.285-719T>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 0.418 in 152,014 control chromosomes in the GnomAD database, including 14,091 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 0.42 (14091 hom., cov: 32)
• Consequence: LOC105372016 XR_935276.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

Genes affected

LOC105372016 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372016	XR_935276.3	n.285-719T>C		intron_variant, non_coding_transcript_variant
LOC105372016	XR_935277.4	n.284-8483T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63418 AN: 151896 Hom.: 14068 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.418 AC: 63501 AN: 152014 Hom.: 14091 Cov.: 32 AF XY: 0.422 AC XY: 31335 AN XY: 74308

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.424

Alfa AF: 0.361 Hom.: 10809

Bravo AF: 0.432

Asia WGS AF: 0.506 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.71
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7239116; hg19: chr18-19486725;