rs13148678

Positions:

• chr4-72993179-T-C
• chr4-72993179-T-G

Variant summary

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

The XR_938873.2(LOC105377273):​n.281-3890T>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 0.143 in 152,028 control chromosomes in the GnomAD database, including 1,848 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 0.14 (1848 hom., cov: 32)
• Consequence: LOC105377273 XR_938873.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

Genes affected

LOC107986286 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986286	XR_001741718.1	n.205+1061A>G		intron_variant, non_coding_transcript_variant
LOC105377273	XR_938873.2	n.281-3890T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21800 AN: 151910 Hom.: 1849 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0947

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.143 AC: 21800 AN: 152028 Hom.: 1848 Cov.: 32 AF XY: 0.144 AC XY: 10677 AN XY: 74298

Gnomad4 AFR AF: 0.0791

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.0947

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.171

Alfa AF: 0.142 Hom.: 295

Bravo AF: 0.151

Asia WGS AF: 0.261 AC: 907 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13148678; hg19: chr4-73858896;