rs947420

Variant names:

• chr1-69549303-C-T
• rs947420
• XR_001738106.2:n.1308-212C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001738106.2(LOC105378789):​n.1308-212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,914 control chromosomes in the GnomAD database, including 7,356 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 0.30 (7356 hom., cov: 32)
• Consequence: LOC105378789 XR_001738106.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 6 publications found

Genes affected

LOC105378789 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378789	XR_001738106.2	n.1308-212C>T		intron_variant	Intron 5 of 11
LOC105378789	XR_007066165.1	n.1308-212C>T		intron_variant	Intron 5 of 11
LOC105378789	XR_007066166.1	n.1308-212C>T		intron_variant	Intron 5 of 12
LOC105378789	XR_947488.3	n.1308-212C>T		intron_variant	Intron 5 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46204 AN: 151798 Hom.: 7344 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.304 AC: 46252 AN: 151914 Hom.: 7356 Cov.: 32 AF XY: 0.302 AC XY: 22386 AN XY: 74240

African (AFR) AF: 0.223 AC: 9247 AN: 41454

American (AMR) AF: 0.304 AC: 4623 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3466

East Asian (EAS) AF: 0.386 AC: 1995 AN: 5162

South Asian (SAS) AF: 0.233 AC: 1125 AN: 4826

European-Finnish (FIN) AF: 0.291 AC: 3074 AN: 10570

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23559 AN: 67906

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.315 Hom.: 1267

Bravo AF: 0.303

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.44
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs947420; hg19: chr1-70014986; COSMIC: COSV59953744;