3-6214310-T-C

Position:

• chr3-6214310-T-C

Variant summary

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

The ENST00000435651.1(ENSG00000226022):​n.95+65732T>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 0.189 in 150,590 control chromosomes in the GnomAD database, including 2,817 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 0.19 (2817 hom., cov: 31)
• Consequence: ENST00000435651.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376942	XR_940578.3	n.781-600T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435651.1	n.95+65732T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28513 AN: 150502 Hom.: 2816 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.189 AC: 28522 AN: 150590 Hom.: 2817 Cov.: 31 AF XY: 0.187 AC XY: 13759 AN XY: 73394

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0570

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.177

Alfa AF: 0.201 Hom.: 5073

Bravo AF: 0.194

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.6
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6774280; hg19: chr3-6255997;