rs7770731

chr6-14598589-T-C

Variant summary

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

The ENST00000414740.2(ENSG00000229646):n.61-990A>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 0.281 in 152,110 control chromosomes in the GnomAD database, including 7,233 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 0.28 (7233 hom., cov: 32)
• Consequence: ENST00000414740.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

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 (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928354	XR_241980.4	n.224-990A>G		intron_variant, non_coding_transcript_variant
LOC101928354	XR_001743992.2	n.362-990A>G		intron_variant, non_coding_transcript_variant
LOC101928354	XR_007059472.1	n.284-990A>G		intron_variant, non_coding_transcript_variant
LOC101928354	XR_926516.3	n.187-990A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000414740.2	n.61-990A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42679 AN: 151992 Hom.: 7219 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.281 AC: 42732 AN: 152110 Hom.: 7233 Cov.: 32 AF XY: 0.280 AC XY: 20816 AN XY: 74372

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.264

Alfa AF: 0.220 Hom.: 6696

Bravo AF: 0.283

Asia WGS AF: 0.338 AC: 1175 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	3.5
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7770731; hg19: chr6-14598820;