rs12978960

Positions:

• chr19-35213334-A-G
• chr19-35213334-A-T

Variant summary

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

The XR_935937.2(LOC105372379):​n.509-2301A>G 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 0.903 in 152,054 control chromosomes in the GnomAD database, including 62,206 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 0.90 (62206 hom., cov: 29)
• Consequence: LOC105372379 XR_935937.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

LOC105372379 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372379	XR_935937.2	n.509-2301A>G		intron_variant, non_coding_transcript_variant
LOC105372379	XR_935938.2	n.397-2301A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137239 AN: 151936 Hom.: 62148 Cov.: 29

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.903 AC: 137358 AN: 152054 Hom.: 62206 Cov.: 29 AF XY: 0.904 AC XY: 67141 AN XY: 74312

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.915

Alfa AF: 0.901 Hom.: 7685

Bravo AF: 0.904

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12978960; hg19: chr19-35704237;