chr6-74161515-A-G

Position:

• chr6-74161515-A-G

Variant summary

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

The NR_110856.1(LOC101928516):​n.138+91927A>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 0.412 in 151,926 control chromosomes in the GnomAD database, including 14,990 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 0.41 (14990 hom., cov: 32)
• Consequence: LOC101928516 NR_110856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928516	NR_110856.1	n.138+91927A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435946.1	n.138+91927A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62611 AN: 151808 Hom.: 14973 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.412 AC: 62665 AN: 151926 Hom.: 14990 Cov.: 32 AF XY: 0.414 AC XY: 30749 AN XY: 74242

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.401

Alfa AF: 0.350 Hom.: 4725

Bravo AF: 0.430

Asia WGS AF: 0.370 AC: 1282 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6912405; hg19: chr6-74871231;