1-34627992-G-T

Position:

• chr1-34627992-G-T

Variant summary

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

The XR_001737964.2(LOC105378641):​n.156-12297C>A 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 0.0981 in 152,170 control chromosomes in the GnomAD database, including 967 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 (967 hom., cov: 32)
• Consequence: LOC105378641 XR_001737964.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

LOC105378641 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378641	XR_001737964.2	n.156-12297C>A		intron_variant, non_coding_transcript_variant
LOC105378641	XR_001737965.2	n.156-12297C>A		intron_variant, non_coding_transcript_variant
LOC105378641	XR_001737966.2	n.156-12297C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14907 AN: 152052 Hom.: 960 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0694

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0981 AC: 14928 AN: 152170 Hom.: 967 Cov.: 32 AF XY: 0.101 AC XY: 7484 AN XY: 74398

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.0536

Gnomad4 OTH AF: 0.0934

Alfa AF: 0.0638 Hom.: 908

Bravo AF: 0.0975

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2093880; hg19: chr1-35093593; COSMIC: COSV59937445;