1-192790056-T-G

Position:

• chr1-192790056-T-G

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.105-23862A>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 0.0984 in 152,058 control chromosomes in the GnomAD database, including 954 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 0.098 (954 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371665	XR_922383.2	n.225+2243A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.105-23862A>C		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-23862A>C		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.369+2243A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14953 AN: 151940 Hom.: 952 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0984 AC: 14963 AN: 152058 Hom.: 954 Cov.: 32 AF XY: 0.0960 AC XY: 7135 AN XY: 74326

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0760

Gnomad4 SAS AF: 0.0438

Gnomad4 FIN AF: 0.0310

Gnomad4 NFE AF: 0.0715

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0805 Hom.: 776

Bravo AF: 0.109

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16834831; hg19: chr1-192759186;