chr1-160647341-T-A

Position:

• chr1-160647341-T-A

Variant summary

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

The XR_001738266.2(LOC107985220):​n.327+6T>A variant causes a splice donor region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0953 in 176,178 control chromosomes in the GnomAD database, including 1,132 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 0.095 (929 hom., cov: 31)
  • Exomes 𝑓: 0.099 (203 hom.)
• Consequence: LOC107985220 XR_001738266.2 splice_donor_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

LOC107985220 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985220	XR_001738266.2	n.327+6T>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14378 AN: 151996 Hom.: 928 Cov.: 31

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0933

GnomAD4 exome AF: 0.0991 AC: 2384 AN: 24064 Hom.: 203 Cov.: 0 AF XY: 0.0982 AC XY: 1234 AN XY: 12562

Gnomad4 AFR exome AF: 0.0660

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.0269

Gnomad4 EAS exome AF: 0.329

Gnomad4 SAS exome AF: 0.0854

Gnomad4 FIN exome AF: 0.116

Gnomad4 NFE exome AF: 0.0705

Gnomad4 OTH exome AF: 0.0830

GnomAD4 genome AF: 0.0947 AC: 14399 AN: 152114 Hom.: 929 Cov.: 31 AF XY: 0.0985 AC XY: 7326 AN XY: 74384

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.0965

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0400 Hom.: 29

Bravo AF: 0.0926

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295614; hg19: chr1-160617131;