1-38434971-G-A

Position:

• chr1-38434971-G-A

Variant summary

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

The XR_947210.3(LOC105378657):​n.424+65025C>T 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 0.35 in 152,032 control chromosomes in the GnomAD database, including 9,799 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 0.35 (9799 hom., cov: 33)
• Consequence: LOC105378657 XR_947210.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

Genes affected

LOC107984943 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984943	XR_001737993.2	n.405+6232C>T		intron_variant, non_coding_transcript_variant
LOC105378657	XR_947210.3	n.424+65025C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53270 AN: 151914 Hom.: 9799 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.350 AC: 53285 AN: 152032 Hom.: 9799 Cov.: 33 AF XY: 0.350 AC XY: 25969 AN XY: 74286

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.369

Alfa AF: 0.393 Hom.: 19488

Bravo AF: 0.337

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7530233; hg19: chr1-38900643;