rs7749983

Positions:

• chr6-129553210-T-A

Variant summary

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

The ENST00000665046.1(ENSG00000226149):​n.139+4848A>T 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 0.196 in 152,082 control chromosomes in the GnomAD database, including 3,005 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 0.20 (3005 hom., cov: 32)
• Consequence: ENST00000665046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723409	XR_001743860.2	n.11509+4848A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665046.1	n.139+4848A>T		intron_variant, non_coding_transcript_variant
	ENST00000657779.1	n.157+4848A>T		intron_variant, non_coding_transcript_variant
	ENST00000670413.1	n.157+4848A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29756 AN: 151964 Hom.: 3001 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.196 AC: 29792 AN: 152082 Hom.: 3005 Cov.: 32 AF XY: 0.194 AC XY: 14414 AN XY: 74328

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.168

Alfa AF: 0.177 Hom.: 304

Bravo AF: 0.201

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7749983; hg19: chr6-129874355;