7-137023221-T-C

Position:

• chr7-137023221-T-C

Variant summary

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

The NR_046103.1(LOC349160):​n.341+9573A>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 0.556 in 151,576 control chromosomes in the GnomAD database, including 24,805 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 0.56 (24805 hom., cov: 32)
• Consequence: LOC349160 NR_046103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC349160	NR_046103.1	n.341+9573A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586239.5	n.273+9573A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84170 AN: 151458 Hom.: 24774 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.556 AC: 84239 AN: 151576 Hom.: 24805 Cov.: 32 AF XY: 0.550 AC XY: 40703 AN XY: 74064

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.550

Alfa AF: 0.533 Hom.: 8964

Bravo AF: 0.551

Asia WGS AF: 0.235 AC: 810 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.49
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10246819; hg19: chr7-136707968;