19-41648308-T-C

Position:

• chr19-41648308-T-C

Variant summary

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

The XR_935972.1(LOC105372405):​n.170+3194A>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 0.551 in 151,866 control chromosomes in the GnomAD database, including 23,153 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 0.55 (23153 hom., cov: 31)
• Consequence: LOC105372405 XR_935972.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

Genes affected

LOC105372405 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372405	XR_935972.1	n.170+3194A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83607 AN: 151748 Hom.: 23136 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.551 AC: 83669 AN: 151866 Hom.: 23153 Cov.: 31 AF XY: 0.552 AC XY: 40958 AN XY: 74204

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.580

Alfa AF: 0.557 Hom.: 31977

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2109075; hg19: chr19-42152229;