rs1923475

Positions:

• chr6-39970688-A-G

Variant summary

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

The ENST00000649703.1(ENSG00000293066):​n.184-9404A>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 0.0614 in 152,282 control chromosomes in the GnomAD database, including 541 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 0.061 (541 hom., cov: 32)
• Consequence: ENST00000649703.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723789	XR_001744112.1	n.260-4032A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649703.1	n.184-9404A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0613 AC: 9328 AN: 152164 Hom.: 539 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0761

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.00583

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0614 AC: 9344 AN: 152282 Hom.: 541 Cov.: 32 AF XY: 0.0610 AC XY: 4544 AN XY: 74458

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0762

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.00583

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0430 Hom.: 53

Bravo AF: 0.0701

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923475; hg19: chr6-39938427;