rs1247318

Positions:

• chr6-160912905-G-C

Variant summary

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

The ENST00000405580.2(ENSG00000220913):​n.440-576G>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 0.175 in 152,094 control chromosomes in the GnomAD database, including 2,409 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 0.17 (2409 hom., cov: 32)
• Consequence: ENST00000405580.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378093	XR_943196.1	n.162+2874C>G		intron_variant, non_coding_transcript_variant
LOC105378093	XR_943195.1	n.187+2874C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000405580.2	n.440-576G>C		intron_variant, non_coding_transcript_variant
	ENST00000650447.1	n.157+2874C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26572 AN: 151976 Hom.: 2406 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.175 AC: 26590 AN: 152094 Hom.: 2409 Cov.: 32 AF XY: 0.179 AC XY: 13313 AN XY: 74356

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.171

Alfa AF: 0.172 Hom.: 280

Bravo AF: 0.166

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1247318; hg19: chr6-161333937;