rs4716272

Positions:

• chr6-18497461-G-C

Variant summary

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

The XR_926549.3(LOC105374955):​n.147+455G>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 0.202 in 151,962 control chromosomes in the GnomAD database, including 3,167 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 0.20 (3167 hom., cov: 32)
• Consequence: LOC105374955 XR_926549.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

LOC105374955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374955	XR_926549.3	n.147+455G>C		intron_variant, non_coding_transcript_variant
LOC105374955	XR_926548.3	n.147+455G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30686 AN: 151844 Hom.: 3171 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0862

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.202 AC: 30694 AN: 151962 Hom.: 3167 Cov.: 32 AF XY: 0.201 AC XY: 14948 AN XY: 74258

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0859

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.204

Alfa AF: 0.209 Hom.: 421

Bravo AF: 0.208

Asia WGS AF: 0.118 AC: 410 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	8.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4716272; hg19: chr6-18497692;