rs2185503

chr6-8349278-T-C

Variant summary

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

The ENST00000670476.1(ENSG00000234763):n.229-6630A>G 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 0.348 in 152,076 control chromosomes in the GnomAD database, including 10,052 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 0.35 (10052 hom., cov: 32)
• Consequence: ENST00000670476.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670476.1	n.229-6630A>G		intron_variant, non_coding_transcript_variant
	ENST00000651914.1	n.312-6630A>G		intron_variant, non_coding_transcript_variant
	ENST00000655767.1	n.342-6630A>G		intron_variant, non_coding_transcript_variant
	ENST00000661402.1	n.425-6630A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52881 AN: 151958 Hom.: 10038 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.348 AC: 52927 AN: 152076 Hom.: 10052 Cov.: 32 AF XY: 0.339 AC XY: 25221 AN XY: 74348

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.381

Alfa AF: 0.320 Hom.: 16924

Bravo AF: 0.360

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2185503; hg19: chr6-8349511;