rs56397626

chr19-50843266-A-G

Variant summary

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

The NR_131205.1(LOC105372441):n.231-7645A>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 0.118 in 152,248 control chromosomes in the GnomAD database, including 1,325 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 0.12 (1325 hom., cov: 32)
• Consequence: LOC105372441 NR_131205.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372441	NR_131205.1	n.231-7645A>G		intron_variant, non_coding_transcript_variant
LOC105372441	NR_131203.1	n.214-7645A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598079.1	n.214-7645A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17905 AN: 152130 Hom.: 1321 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.118 AC: 17938 AN: 152248 Hom.: 1325 Cov.: 32 AF XY: 0.114 AC XY: 8491 AN XY: 74440

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0728

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0949

Gnomad4 OTH AF: 0.127

Alfa AF: 0.109 Hom.: 144

Bravo AF: 0.125

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.5
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56397626; hg19: chr19-51346522;