rs6770515

Positions:

• chr3-193772960-A-G
• chr3-193772960-A-T

Variant summary

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

The ENST00000664530.1(ENSG00000287206):​n.565+522A>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 0.551 in 152,048 control chromosomes in the GnomAD database, including 23,748 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 0.55 (23748 hom., cov: 32)
• Consequence: ENST00000664530.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664530.1	n.565+522A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83726 AN: 151930 Hom.: 23729 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.551 AC: 83796 AN: 152048 Hom.: 23748 Cov.: 32 AF XY: 0.557 AC XY: 41371 AN XY: 74324

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.546

Alfa AF: 0.577 Hom.: 5378

Bravo AF: 0.534

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6770515; hg19: chr3-193490749;